Input is keyword driven with sensible defaults in most cases. Free format may be used within each line. Blank lines are ignored.

The following keywords are recognised, where *n* and *x* are integer and
real data, respectively.

*2D*: enforce two-dimensional `flatland'.*A9INTE*: specifies that after each quench that does not lead to an inversion of chirality, isomerisation of a peptide bond or cold fusion - the interaction enthalpy between a specified residue and the rest of the system should be calculated using the external script `AMBGMINintE.sh', and read back into GMIN. This is intended for use with protein/ligand systems where you are searching for low energy docked structures. As the total energy does not fully correlate with the protein/ligand interaction enthalpy, it is often useful to retain not only the lowest*SAVE*total energy structures, but also the lowest*SAVEINTE*interaction enthalpy structures. To use this keyword, the `AMBGMINintE.sh' script (contained in the SVN repository in the SCRIPTS directory) must be present in the GMIN working directory. You should ensure that you have edited it to match the residue numbering of your system. You also need a full AMBER9+ installation with access to the `sander' executable. When using this keyword, an interaction enthalpy dump file is produced every*DUMPINT*steps, and at the end of the run, structural output files are produced for the*SAVEINTE*lowest interaction enthalpy geometries. After each quench, the structure with the current lowest interaction energy is dumped in pdb and rst format prefixed with `bestint.' to allow monitoring.*ACCEPTRATIO accrat*:*accrat*is the required acceptance ratio for the MC exploration of the transformed surface. For fixed temperature runs (the default) the maximum step size is adjusted to try and meet the requested value of*accrat*; for a fixed maximum step size the temperature is adjusted instead. The default value of*accrat*is a half.*ACE step*: used for regular Born radii updates in CHARMM every*step*steps.*ACKLAND id*: specifies an Ackland embedded atom metal potential coded by Dr Mihai-Cosmin Marinica.*id*specifies the particular metal: 1 is ?, 2 is ?, 3 is ?, 4 is ?, 5 is iron, 6 is a different iron, 7 is tungsten. Positive values for*id*specify periodic boundary conditions, where box lengths must be specified by the*PERIODIC*keyword. Negative values for*id*specify a cluster calculation. A*CUTOFF*value can also be used for clusters.*ACKLAND1*: specifies first iron potential.*ACKLAND2*: specifies second iron potential.*ALGLUE*: specifies a glue potential for aluminium.*ALIGN*: specifies that, before the basin-hopping run, a second set of coordinates should be read in from`finish`, and an alignment operation between the coordinates in`coords`and the set in`finish`is performed. This is very similar to the keywords*PERMOPT*and*PERMINVOPT*, but unlike those it doesn't require that permutations be specified. Because of the way those keywords are set up, the minimised distance between the two structures is returned as an ''energy'' and therefore will cause an error when the basin-hopping run starts. For this reason,*ALIGN*should not be used with non-zero*STEPS*. This keyword should only be used for testing alignment algorithms.`OPTIM`is the appropriate tool for aligning structures.*AMBER12*: specifies calculation with the interfaced version of the AMBER 12`pmemd`program. AMBER 12 requires an additional input file,`min.in`, which specifies keywords for the AMBER 12 potential. It also requires appropriate topology and coordinates, in files named`coords.prmtop`and`coords.inpcrd`respectively. For details, see the AMBER 12 manual. As with the AMBER 9 interface, cutoffs are smoothed, using the`minin`keyword`ifswitch=1`. Additional keywords are as AMBER9, with the exception of*AMBERMDSTEPS*, which is not implemented.*AMBER9 inpcrd inpcrdformat*: specifies a calculation with the interfaced version of the Amber 9 program package. From this package the Amber force fields are being used, with small modifications (*e.g.*smooth cut-offs). Starting coordinates do not need to be specified in the*odata*file, they are read from*inpcrd*instead (default*coords.inpcrd*), in Amber inpcrd file format specified by the second optional argument*inpcrdformat*. If the second argument is missing, it is assumed that*inpcrd*contains only three columns with the xyz coordinates of all atoms, in the same order as in the topology file. To start a run with this interface, several auxiliary files are required in the same directory: input coordinate file*coords.inpcrd*, parameter topology file*coords.prmtop*, input file to Amber containing force field specifications*min.in*, and, if desired, a coordinate file different from*coords.inpcrd*containing starting coordinates. To turn on smooth cutoffs for the Generalised Born force fields, the keyword*ifswitch=1*has to be used in the*&cntrl*namelist block of*min.in*. When using the*AMBER9*keyword, any calculated second derivatives will be numerical. If one wants analytical second derivatives, the*NAB*keyword should be used instead, with the same syntax. Additional keywords for the AMBER 9 runs are*DUMPSTRUCTURES*,*AMBERMDSTEPS*,*LIGMOVE*,*BLOCKMOVE*and*MOVABLEATOMS*.*AMBERENERGIES*dump energy components for AMBER at every step.*AMBERMDSTEPS*MD steps for AMBER9 as propagation steps in basin-hopping. Rather inefficient method.*AMBERMUTATION nmut ntest*Mutational steps coupled with group rotations for AMBER12.*nmut*is the frequency of mutational steps attempted, and*ntest*the number of steps after the mutation before a Metropolis criterion is applied to accept or reject the mutation.*AMBERMUTENERGY opt1 opt2*Specifies what energy or penalty function should be used to accept or reject mutations.*opt1*can be 1 (random number, for testing), 2 (a component of the AMBER energy, e.g. solvation energy;*opt2*specifying which term), 3 (interaction energy between two molecules,*opt2*is the last residue of the first molecule), and 4 to 7 for various geometrical measures for helices.*AMBERMUTFF ff*The used force field to recreate the topology files as needed,*ff*is currently implemented for 99 (ff99SB) and 14 (ff14SB).*AMBERMUTIGB igb*Solvent model used.*igb*is either 2 or 8.*AMBERMUTRIGID**AMCHNMAX*: The maximum number of angles that will be changed by up to*STEP*during an AMBER dihedral step. If this is not set or is set to zero, cartesian steps of maximum size*STEP*are taken instead.*AMCHNMIN*: The minimum number of angles that will be changed during an AMBER dihedral step.*AMCHPMAX*: The maximum probability for a single angle to be twisted in an AMBER dihedral step.*AMCHPMIN*: The minimum probability for a single angle to be twisted in an AMBER dihedral step.*AMH*Associative Memory Hamiltonian protein model.*ANGSTROM*: specifies coordinates in Ångstrom for the*FRAUSI*potential.*ARGON*: introduces a diatomics-in-molecules calculation for a neutral, cationic or electronically excited argon cluster. See also*GROUND*,*PLUS*,*TWOPLUS*and*STAR*.*ARM arma armb*: use the acceptance-ratio method (Bouzida et al.,*Phys. Rev. A*,**45**, 8894, 1992) to adjust the step size to achieve the requested acceptance ratio. A scaling factor is calculated and applied to*step*,*rotmax*, and/or*transmax*. The scaling factor is calculated according to , where defines the target acceptance ratio and the actual acceptance ratio. Both values*arma*and*armb*default to 0.4.*ARNO*: specifies a diatomics-in-molecules potential for Ar-NO clusters.*AVOID dist maxsave*: specifies that the geometry should be reseeded if the latest structure gets within a distance*dist*of the*maxsave*members of a cyclic list. If a third argument `F' is added to the*AVOID*line then such steps are simply rejected rather than reseeded. The*NEWRESTART*keyword must be specified to populate the list of minima to be avoided. If the `F' argument appears for*AVOID*then*NEWRESTART*will not reseed.*AXTELL zstar*: specifies an additive Axilrod-Teller term for certain diatomics-in-molecules potentials as well as the Pacheco-Ramelho intermolecular potential for C.[8]*zstar*is the coefficient multiplying this term.*BASIN bgmax*: specifies a basin-hopping run (as opposed to standard MC on the untransformed surface).*bgmax*is the convergence threshold on the RMS force in the basin-hopping quenches. If this criterion is too strict then the run time will be greatly increased. If it is too sloppy then the performance of the algorithm is impaired. Different values are needed for different potentials.*SLOPPYCONV*can be used instead.*BENZRIGIDEWALD ewaldrealc ewaldrecipc*: calls anisotropic potential developed by [9] for periodic systems of rigid benzene molecules and uses Ewald summation to compute the long-range electrostatics.*ewaldrealc*and*ewaldrecipc*specify the real-space and reciprocal-space cutoff values for the Ewald summation. The cell dimensions should be specified using the*PERIODIC*keyword. This potential works for both orthorhombic and triclinic cells. Also, the*RIGIDINIT*keyword must be specified. Also, the energy gradient with respect to cell parameters is computed if the*BOXDERIV*keyword is used.*BFGS*: specifies that the full BFGS minimiser should be used. Inefficient compared to LBFGS.*BGUPTAT NTYPEA AAA PAA QAA ZAA R0AA*: One of the required keywords to specify a Binary Gupta run. NTYPEA is specified, followed by the potential parameters for the A-A interactions. See also BGUPTATAB and BGUPTATBB. [NB: Per-atom energies will be stored.]*BGUPTATAB AAB PAB QAB ZAB R0AB*: The line to specify the potential parameters for the A-B interactions for a Binary Gupta run.*BGUPTATBB ABB PBB QBB ZBB R0BB*: Specifies the B-B interaction parameters.*BGUPTANAME name1 name2*: specifies the names of species A and B for a Binary Gupta run. Default are Au and Ag.*BHPT pttmin pttmax exchprob*(*random**interval*) (*single**sets*): specifies a parallel tempering basin-hopping run with temperatures exponentially distributed between*pttmin*and*pttmax*. Either the probability of attempting replica exchange (float, ) or the corresponding mean frequency (integer, ) may be supplied as*exchprob*. Exchanges may be attempted at random or at intervals (default: random). At each exchange event, either a single exchange between a random pair adjacent replicas is attempted, or exchange between all pairs in either the set of even pairs, or set of odd pairs, (default: single). Should be used together with the*MPI*keyword. (Only available if the source is compiled with MPI enabled.) If*DUMPSTRUCTURES*is specified, then every*DUMPINT*steps, minima from each replica will the written out in XYZ format to files`dumpmin.replicaNumber.minimaNumber`.*BLOCKMOVE nblocks block_1 block_2 ... block_n*: used with*AMBER9*,*MOVABLEATOMS*and*LIGMOVE*. Divides the atom list in the ‘movableatoms' file into*nblocks*distinct blocks that are treated independently as rigid during steptaking moves.*block_i*specifies the number of atoms in each block. Step size parameters for rigid rotation, translation and cartesian moves are taken from the parameters of*LIGMOVE*.*BINARY ntypea epsab epsbb sigmaab sigmabb*: specifies a binary Lennard-Jones system.*ntypea*is the number of type A atoms--the rest are assumed to be type B and appear at the end of the list of coordinates. define the units of energy and length, and*epsab*= ,*epsbb*= ,*sigmaab*= ,*sigmabb*= . The box parameters and cutoff should be specified with the*PERIODIC*keyword.*BINARY_EXAB freq*: attempt exchange move for an A and a B particle every*freq*steps.*BINSTRUCTURES SaveNth*: requests that the geometry of every*SaveNth*new structure found during basin-sampling is recorded in`binstructures.j`, where*j*is the index of the bin to which a given minimum belongs. If this keyword is present then GMIN switches from plain PTMC to BSPT. Without*BINSTRUCTURES*the*BSPT*keyword will perform a standard PTMC run with no quenching.*BLJCLUSTER ntypea epsab epsbb sigmaab sigmabb cutoff*: specifies a binary Lennard-Jones cluster. The parameters are the same as for*BINARY*, above.*BLJCLUSTER_NOCUT ntypea epsab epsbb sigmaab sigmabb*: specifies a binary Lennard-Jones cluster without a distance cutoff. More efficient than*BLJCLUSTER*for smaller systems. The parameters are the same as for*BINARY*, above. [NB: Per-atom energies will be stored.]*BLN*: specifies a BLN off-lattice protein model with bond-length and bond-angle force constants and . An auxiliary file`BLNsequence`is required. See §6.2 for more details.*BLNGO*: specifies a Go potential with the same form as the*BLN*potential. The parameters and are the same as those used for the*BLN*keword and a`BLNsequence`file is required. Also needed is an auxiliary file,`contactmap`, containing the pairs of residues in contact in the native state of the protein with one pair of residue numbers in each line of the file. An optional parameter, , specifies the strength of the non-native interactions in a scaled*BLN*potential [10].*BOXCENTROID x y z dx dy dz (ix iy iz)*: confine the system centroid to region*(xdx, ydy, zdz)*. Intended for systems interacting with an external field, e.g. a cluster supported on a substrate modelled using keyword*MIE_FIELD*. The cluster centroid will be checked after each random perturbation (before quenching!), and on each step of the*QALCS_SURF*procedure (if used, and also before quenching). When a centroid coordinate (say*x_c*) ventures outside the corresponding range (*xdx*), that centroid coordinate is translated back to*x*. If any of the optional integer parameters*(ix, iy, iz)*are set to unity (default value is zero), then the translation vector(s) in the corresponding direction(s) will be restricted to integer multiples of*dx*and/or*dy*and/or*dz*. This additional feature is intended for periodic external fields, e.g. a periodic substrate, in which case*dx/dy/dz*ought to match the period.*BOXDERIV boxlx boxly boxlz alpha beta gamma*: computes the energy gradient with respect to cell lengths and angles for periodic systems where the unit cell parameters are also optimized.*boxlx, boxly, boxlz, alpha, beta, gamma*are the box lengths and angles, in radians, of the initial structure. If only the box lengths are given, the cell will be taken as orthorhombic, and only the cell lengths will be optimized. The cell lengths and angles of the initial structure should also be specified using the*PERIODIC*keyword. If the gradients wrt cell parameters are being calculated for a system using atomic, Cartesian coordinates, the initial coordinates in the`coords`file should be in fractional coordinates. If the gradients wrt cell parameters are being calculated for a system using rigid body coordinates, the initial coordinates coordinates should be given in the usual way for GENRIGID, and the*RIGIDINIT*keyword should be used.*BOXSTEP boxstepfreq*: for use with the framework for optimizing cell parameters using the*BOXDERIV*keyword. Randomly changes the cell lengths and angles every*boxstepfreq*basin-hopping stes.*BRANCHNBOUND N*: Specify the use of the GO-PERMDIST alignment algorithm described in Griffiths et al.,*JCTC*2017. This algorithm overrides the default MINPERMDIST alignment subroutine. GO-PERMDIST uses a branch and bound algorithm combined with the older PERMDIST method for combined translation-rotation alignments. It can be used for either periodic or aperiodic systems. Use of GO-PERMDIST is recommended for aperiodic systems, but for periodic it can be very slow, and use of the FASTOVERLAP keyword is recommended instead.

GO-PERMDIST is deterministic and, if allowed to run indefinitely, will guarantee identification of the best alignment. In practise it is run with an early exit criterion expressed as a number of iterations*N*. A small value of*N*is often sufficient to identify the best possible alignment but usually insufficient to prove that the identified alignment is the best possible value. The default is 2000, which is generally a reasonable compromise between speed and accuracy.*BSMIN*: specifies a Bulirsch-Stoer minimisation scheme. Very inefficient compared to LBFGS.*BSPT histmin histmax ptemin ptemax pttmin pttmax exchprob nequil ptsteps nquench nenrper hbins qfrq*: requests a basin-sampling run to accumulate the quench probability for local minima as a function of potential energy using a parallel-tempering algorithm. This keyword also specifies the energy range for the histogram of quench energies,*histmin*to*histmax*, the energy range for the histogram of instantaneous configurations,*ptemin*to*ptemax*, the temperature range (*pttmin*and*pttmax*), the probability of attempting an exchange*exchprob*, the number of equilibration steps,*nequil*, the number of parallel tempering MC steps without quenching,*ptsteps*, the number of parallel tempering MC steps with quenching,*nquench*, the number of bins for the histogram of instantaneous potential energy,*nenrper*, the number of bins for the histogram of quench energies,*hbins*, and the quench frequency,*qfrq*. Should be used together with the*MPI*keyword. (This option is only available if the source is compiled with an MPI enabled.)*BSPTDUMPFRQ n*,*n*is the interval at which intermediate statistics and*bsptrestart*files are dumped. If*n*is less than one these files will only be dumped at the end of a complete run. See also*BSPTRESTART*.*BSPTRESTART*: restart a previous*BSPT*or*PTMC*run. The instantaneous and quench potential energy histograms are read from the last`Visits.his`and`Visits2.his`files, and the current state from`bsptrestart`files (one per node, numbered from zero). A finished run can be continued with more steps by changing the*nquench*or*ptsteps*parameters on the*BSPT*or*PTMC*line of the data file. Setting the interval for*BSPTDUMPFRQ*to minus one will read the last set of dump files.*BSPTQRANGE minE maxE*: set minimum (*minE*) and maximum (*maxE*) energies for BSPT quenches.*CALCQ*: turn on calculation of bond order parameters.*CAMSHIFT csversion svnroot shiftfile csn csalpha*: uses chemical shifts as restraints during the optimization procedure. Currently,*CAMSHIFT*can only be used together with*CHARMM*.*csversion*is a string that specifies the method for combining the two potentials: MERGE means , ORIGINAL means , and NOFF means .*svnroot*specifies the svn root directory (e.g., $HOME/svn/).*shiftfile*is the file containing the experimental shifts, which has to be located in the working directory.*csversion*,*svnroot*and*shiftfile*all have to be specified together with*CAMSHIFT*.*csn*and*csalpha*are optional parameters. They define the tolerance parameter of the CamShift energy profile, and the relation between CamShift and the force field, respectively. Default values for both are 1.0.*CAPSID rho epsilon radius height*: specifies a coarse-grained potential to represent virus capsid pentamers with parameters , , and , respectively. If is omitted the default is 0.5.*CENTRE*: if present the system will be translated so that the centre-of-mass lies at the origin after every quench.*CENTREXY*: if present the system will be translated so that the centre-of-mass lies at the centre of the xy plane after every quench. This is useful when using an implicit membrane like IMM1 where you have directionality only in the z-direction, so centreing in x and y should have no delaterious effect.*CG*: specifies a conjugate-gradient minimisation scheme. Inefficient compared to LBFGS.*CHANGEACCEPT naccept*:*naccept*is an integer which sets the interval at which the acceptance ratio is checked and possible adjustments are made to the maximum step size or the temperature. The default is*naccept*.*CHARMM*: specifies that a CHARMM potential should be used. See also keywords*CHARMMTYPE*,*CHPMAX*,*CHPMIN*,*CHNMAX*,*CHNMIN*,*NOPHIPSI*,*TOMEGA*,*INTMIN*,*CHFREQ*,*CHRIGIDROT*,*CHRIGIDTRANS*, and*RMS*. If*CHNMAX*is not specified, a cartesian displacement step taking scheme will be used. For cartesian steps, rings are moved as rigid bodies to avoid false knotted minima. See*RINGROTSCALE*. Finally, Molecular Dynamics (MD) can be employed to generate new geometries. See*CHMD**CHARMMDFTB*: specifies that the CHARMM SCC-DFTB potential is to be used, and disables updates of the nonbonded list. This assumes you are using a fully QM system. If you are using a QM/MM setup, you should not use this keyword! Note that SCC-DFTB can only be used with CHARMM35.*CHMD CHMDFREQ*: Requests Molecular Dynamics (MD) runs to be performed every*CHMDFREQ*step to generate new geometries. A*CHMDFREQ*setting of 20 will execute an MD run every 20 step, while dihedral or cartesian moves are applied otherwise as specified in the data file. A CHARMM parameter file named 'chmd.par' containing all relevant keywords for the CHARMM*DYNA*module has to be present in the working directory. All CHARMM keywords must be uppercase and given in the first line. A typical example is:VERL NSTEP 500 TIMESTEP 0.002 TWINDH 10.0 IEQFRQ 200 ICHECW 1 IASORS 0 IASVEL 1 FIRS 500 FINA 500

Please consult the CHARMM manual for further details on the

*DYNA*module. Currently, the length of the input string given in 'chmd.par' is limited to 500 characters.*CHARMMENERGIES*: prints the components of the total CHARMM energy after each step.*CHARMMTYPE topfile paramfile*:*topfile*and*paramfile*are the common CHARMM top and param files , e.g., `toph19_eef1_perm.inp' and `param19_eef1_perm.inp'.*CHFREQ nfreq*: used with*CHARMM*keyword to specify that every*nfreq*basin-hopping steps dihedrals are twisted. Default is*nfreq*=1.*CHNMAX*: used with*CHARMM*keyword to specify the maximum allowed number of angles to be twisted. Specifies a dihedral angle step taking scheme.*CHNMIN*: used with*CHARMM*keyword to specify the minimum allowed number of angles to be twisted.*CHPMAX*: used with*CHARMM*keyword to specify the maximum allowed probability for twisting an angle.*CHPMIN*: used with*CHARMM*keyword to specify the minimum allowed probability for twisting an angle.*CHRIGIDROT prot rotmax nrot*: used with*CHARMM*keyword to support rigid body rotation every*nrot*basin-hopping steps with maximum allowed probability*prot*and maximum allowed rotation angle*rotmax*(in degrees). The keyword*CHRIGIDROT*requires a file`segments.tomove`, which specifies the segments for rigid rotation. The segments are numbered and each line contains only one number.*CHRIGIDTRANS ptrans transmax ntrans*: used with*CHARMM*keyword to support rigid body translation every*ntrans*basin-hopping steps with maximum allowed probability*ptrans*and maximum allowed translation*transmax*(in Å). The keyword*CHRIGIDTRANS*requires a file`segments.tomove`, which specifies the segments for rigid translation. The segments are numbered and each line contains only one number.*CHRIGIDROT*and*CHRIGIDTRANS*use the same`segments.tomove`.*CHECKD n*: calculates gradients analytically and numerically for the initial coordinates, then exits. is an integer optional argument; if equal to zero, then only the single-point energy is calculated and reported.*CISTRANS*: disables all checks for cis or deformed amide/peptide bonds.*CHIRO*: calls the OK potential. If is absent or 0, then use one LJ site. If , use LJ-like rods of length . Output is written to`chiro.xyz`. A periodic boundary condition in the direction can be applied using the*PERIODIC*keyword.*CNBH*: a critical nucleus basin-hopping run. As for*FEBH*(must also be set) but the accept/reject move for sizes is based on the minimum partition function (maximum free energy) for competing sizes. This is the superposition sum for all the known distinct minima of the corresponding sizes.*COLDFUSION thresh*: if the energy falls below threshold*thresh*then cold fusion is assumed to have occurred and geometry optimisation stops. The default value is .*COMPRESS kcomp*: add a harmonic compression potential with force constant*kcomp*using the centre-of-mass distance for each atom. The compression term can be turned off once a given RMS tolerance is achieved using the*GUIDE*keyword. This combination can be used with the generalised rigid body scheme introduced via the*RIGIDINIT*keyword.*COMPRESSRIGID kcomp dist*: if at least one rigid body's centre of mass is further than*dist*from its nearest neighbour, add a harmonic compression potential with force constant*kcomp*using the centre-of-mass distance for each rigid body. The compression is disabled once the rigid bodies are all within*dist*of another. This keyword is only implemented for a few specific potentials. However, the*COMPRESS*and*GUIDE*keywords can be used with the general rigid body scheme introcduced via*GENRIGID*.*COMMENT*: the rest of the line is ignored.*COOPMOVE n cut*: specifies cooperative moves in the step-taking routine. An atom is selected at random, and the*n*nearest neighbours (default 5) that lie within a cutoff distance of*cut*(default 1.0) are moved by the same amount.*CPMD sys*: specifies that the CPMD program should be called for energies and gradients. Not tested!*CSM pg opt2 opt3*: continuous symmetry measure from Pinsky, Dryzun, Casanova, Alemany and Avnir,*J. Comp. Chem.*, 29, 2712, 2008. Point group*pg*needs to be specified.*CUDA potential*: specifies a GPU run. Setting*potential*to 'A' specifies the AMBER12 potential. See the group wiki for further information.*CUDATIME*: get timings for CUDA runs (benchmarking).*CUTOFF cutoff*: sets a cutoff beyond which the potential is truncated. This only has an effect for tight-binding silicon at present. Interaction cutoffs for other potentials should be specified in their input files e.g. min.in (and min_md.in if used) for AMBER9 or below the*CHARMM*line for CHARMM.*DAMPEDGROUPMOVES*: damped group moves, the structure is very similar to group rotation moves with appropriate changes.*DBP epsbb sigmabb muD E*: calls a finite system of dipolar Lennard-Jones dumbbells [11], where the electric field of stength can be optionally present. The field, if present, is along the space-fixed z-direction. and are both set to unity by default. is the dipole moment; 's and 's correspond to the Lennard-Jones parameters.*DBRENT*: specifies minimisation using Brent's method with first derivatives in the conjugate-gradient procedure. Inefficient compared to LBFGS.*DEBUG*: sets various debug printing options including the dumping of initial geometries and energies (to*dump.X.xyz*) if*DUMP*is also set.*DECAY x*: magnitude of random move decays according to parameter*x*with distance from a randomly chosen atom.*DF1*: specifies a binary 2D potential. The first atoms have unit radius and the rest have radius 1.4, with a cutoff for each pair type at the average radius. The keyword*2D*must also be specified, along with a*PERIODIC*line to specify two box-lengths. Initial work uses box lengths of 3.31437171 for a number density of 0.9.*DFTB*: specifies a DFT-based tight-binding potential; the multiplicity is specified by keyword*MULTIPLICITY*.*DFTBC*: specifies a DFT-based tight-binding potential carbon. Can be guided using*LJAT*.*DGUESS dguess*: initial guess for diagonal elements of the inverse Hessian, used whenever the LBFGS optimiser is reset. The default is dguess=0.1.*DIHEDRALROTATION*: This keyword performes random rotations of groups about specified dihedral angles. Similar to*GROUPROTATION*, the dihedral groups must be defined in a file named*dihedralgroups*, with the following syntax:

GROUP name type at1 at2 at3 at4 maxrot pselect

gat

gat

gat

Here ``name'' is a string defining the group name; ``type" is a string defining the type of dihedral for backbone rotations (phi, psi etc.), used for printing purposes only; at1 to at4 are integers specifying the atom indices defining the dihedral angle, gat gat define indices of the atoms which rotate, and the number of such atoms.

Note: at4 should also be included in the list of atoms to rotate, as it is the final atom defining the dihedral!*DIPOLES*: causes the first order induction energy to be included in a diatomics-in-molecules calculation for Ne or Ar. By default this term is neglected, although it may be significant.*DMACRYS*: use of DMACRYS for potential calculations.*DONTMOVE n1 n2*: prevents atoms*n1, n2,*moving during MC step taking. They can still move during minimisation.*DONTMOVEGROUP centre radius type*: If*type*is set as default to GT,*DONTMOVEGROUP*prevent all atom greater than*radius*angstroms from the*centre*atom from moving during MC step taking.*type*can also be set to LT to not move all atoms within*radius*of*centre*.*DONTMOVERES n1 n2*: prevents all atoms in residues*n1, n2,*from moving during MC step taking.*DONTMOVEALL n1 n2*: prevents all atoms from moving during MC step taking (usually used with*DOMOVE*and*DOMOVERES*).*DOMOVE n1 n2*: allows atoms*n1, n2,*to move during MC step taking. Only functions in conjunction with*DONTMOVEALL**DOMOVERES n1 n2*: allows all atoms in residues*n1, n2,*to move during MC step taking. Only functions in conjunction with*DONTMOVEALL**DUMP*: if present will cause the energy and quench geometry for every step to be dumped into*dump.X.xyz*where X is an integer. The geometries are saved in XMakemol xyz format. If*CHARMM*is also specified,*dump.pdb*and*dump.crd*are produced containing each quench geometry in PDB and CHARMM CRD format.*DUMP_MARKOV nwait nfreq*: dump the Markov geometry and energy (every*nfreq*trial steps and after the first*nwait*) to file*dump.X.xyz*, where X is an integer. Intended for use**instead**of*DUMP*and in conjunction with*FIXBOTH*to facilitate the characterisation of equilibrium structure as part of post-processing.*DUMPBEST*: dump best structures after every step.*DUMPINT int*: changes the default interval for dumping a restart`GMIN.dump`file from 1000 basin-hopping steps to*int*.*DUMPMIN*: When using more than one processor (e.g.*BHPT*), or in conjunction with*DUMPSTRUCTURES*, the SAVE lowest minima will be dumped every*DUMPINT*steps as dumpmin.x files.*DUMPQU*: when using*AMBER9*, dumps each quench geometry in rst format to quenchX.rst and pdb format to quenchX.pdb. Dumping does not occur if a chirality check fails.*DUMPSTEPS*: when using*AMBER9*, dumps each geometry after the MC step has been taken in rst format to afterstepX.rst and pdb format to afterstepX.pdb.*DUMPSTRUCTURES*: dump best structures in rst, xyz and pdb format.*DUMPUNIQUE*: dump unique structures as soon as they are found.*DZUGUTOV dzp1 dzp2 dzp3 dzp4 dzp5 dzp6 dzp7*: Dzugutov potential in a general form. The parameters are , , , , , and .*EAMAL*: specifies an embedded atom model for aluminium.*EAMLJ A0 beta Z0*: specifies the EAMLJ potential (Baskes,*Phys. Rev. Lett.*,**27**, 2592, 1999) with parameters*A0*,*beta*and*Z0*.*EDIFF econv*: quench minima are only considered to be different if their energies differ by at least . This option mainly affects the lowest energy saved geometries. If the current quench energy is within of a saved energy, but lies lower, then the saved energy and geometry are replaced. The default is but different values are appropriate for different potentials.*ENERGY_DECOMP*: print energy decomposition for AMBER9 and AMBER12*ENPERMS*: Enumerate all distinct permutations of a binary system (0 <NTYPEA <NATOMS) using Lehmer's algorithm. Instead of a traditional geometry-perturbing step, Lehmer's algorithm will generate a new permutationl isomer by swapping the coordinates of two deterministically-picked unlike atoms. The procedure terminates once all the distinct permutations have been enumerated.*EQUILIBRATION equil DumpEveryNthQuench*:*equil*is the number of MC steps preceding the accumulation of the density of states histogram in a Wang-Landau basin-sampling run. The default is 0.*DumpEveryNthQuench*specifies how often the statistics are recorded into the output files.*EWALD N ewaldrealc ewaldrecipc*: computes long-range potentials (such as electrostatics) using Ewald summation.*N*specificies the order of the potential (use 1 for electrostatics).*ewaldrealc*and*ewaldrecipc*are the real-space and reciprocal-space cutoffs. This should only be used with periodic systems, so the*PERIODIC*keyword must be specified.*EXEQ n*: for use with the*RESERVOIR*keyword. After a configuration is taken from the reservoir by the lowest temperature non-reservoir replica we do not record visits statistics for*n*steps. This allows some local equilibration if the configuration is not truely equilibrium.*EXPANDRIGID freq factor (NORMALISE)*: for use with the generalised rigid body framework,*RIGIDINIT*. Expands the system by a factor of*factor*by scaling the distance of each rigid body from the centre of mass of the system every*freq*steps. If the third argument*NORMALISE*is used, all rigid bodies are simply translated by*factor*from the system centre of mass.*EXTRACTFRQS*: extract the normal mode frequencies of minimum*n*from`min.frqs`and write them to file`extractedfrqs`. For use with*USEMINDATA*and*CNBH*.*EXTRACTMIN n*: extract the coordinates of minimum*n*from`points.min`and write them to file`extractedmin`. For use with*USEMINDATA*and*CNBH*.*FAL*: specifies the Farkas potential for aluminium.*FASTOVERLAP N*: Specify the use of the FASTOVERLAP alignment algorithm described in Griffiths et al.,*JCTC*2017. This algorithm overrides the default MINPERMDIST alignment subroutine. FASTOVERLAP uses the FFTW library to quickly maximise the overlap of Gaussian kernels centred on each atom in the two structures being aligned. It can be used for either periodic or aperiodic systems. Use of FASTOVERLAP is recommended for periodic systems, but for aperiodic it can be very slow, and use of the BRANCHNBOUND keyword is recommended instead. FASTOVERLAP is deterministic and systematically improvable.

The alignment procedure is repeated*N*times from different starting positions, and the best alignment is used. For periodic systems, starting positions are generated by applying global translational displacements to one of the structures. For aperiodic systems, global rotations are used.*N*defaults to 1, but larger values can yield improved accuracy for extra computational cost.*is the width of the Gaussian kernel used in the alignment. For a discussion of appropriate values, see the original paper. If left unspecified,**defaults to 1/3 of the average interatomic spacing, which is usually a sensible value. This spacing is determined from the number of particles and box lengths for a periodic system (so the default value will not be suitable if the system is inhomogeneous), and measured directly from the two structures being aligned in the case of an aperiodic system.**is the maximum angular momentum used in SOFT transforms for FASTOVERLAP with aperiodic systems. The default value of 15 should be appropriate for most systems, but a larger value may be required for very large clusters and biomolecules. This parameter has no effect for periodic systems.*

FASTOVERLAP is compatible with the OHCELL keyword to test for unit cell symmetries in cubic periodic systems. Note that, by default, FASTOVERLAP will test inversion isomers for alignment, which may not be appropriate for all systems (especially biomolecules). The NOINVERSION keyword should be specified to avoid this.*FEBH FEBH*: do a free energy basin-hopping run. This uses the free energy calculated using the harmonic superposition approximation for the acceptance criterion. This also leads to rejection of transition states from the Markov chain (GMIN has no in-built check to guarantee this for a potential energy run). Additionally, it enables the*MIN_ZERO_SEP*keyword, which uses the separation of the zero eigenvalues (typically the 6 corresponding to overall translation and rotation) to determine convergence.*FIXEDEND*: requires documentation.*FIXBOTH*: both the temperature and maximum step size are fixed regardless of the calculated acceptance ratio.*FIXCOM*: fix centre of mass rather than centre of coordinates.*FIXSTEP*: the maximum step size is fixed and the temperature is varied to try and achieve the requested acceptance ratio.*FIXTEMP*: explicitly fixes the temperature. Only used if*FIXSTEP*is set, in which case using*FIXTEMP*gives a result equivalent to*FIXBOTH*.*FNI*: specifies the Farkas potential for nickel.*FRAUSI*: specifies a particular tight-binding potential for silicon. See also keyword*ANGSTROM*.*FREEZE n1 n2*: freeze the coordinates of atoms*n1, n2,*. Atoms affected by FREEZE will not move during MC step taking, or during minimisation as their gradients are set to zero. Frozen atoms may also be specified in a file`frozen`. The first line of the file should contain the number of frozen atoms. Subsequent lines contain the atom indices to be frozen.*FREEZEGROUP centre radius type*: If*type*is set as default to GT,*FREEZEGROUP*FREEZEs all atom greater than*radius*angstroms from the*centre*atom.*type*can also be set to LT to FREEZE all atoms within*radius*of*centre*.*FREEZERES n1 n2*: freeze the coordinates of all atoms in residues*n1, n2,*.*FREEZEALL n1 n2*: freeze the coordinates of all atoms*UNFREEZE n1 n2*: unfreeze the coordinates of atoms*n1, n2,*. Only functions in conjunction with*FREEZEALL**UNFREEZERES n1 n2*: unfreeze the coordinates of all atoms in residues*n1, n2,*. Only functions in conjunction with*FREEZEALL**FS gatom*: specifies a Finnis-Sinclair potential using parameters from Finnis and Sinclair,*Phil. Mag. A*,**50**, 45 (1984) and corresponding erratum*Phil. Mag. A*, 53, 161 (1986).*gatom*=1 for V,*gatom*=2 for Nb,*gatom*=3 for Ta,*gatom*=4 for Cr,*gatom*=5 for Mo,*gatom*=6 for W,*gatom*=7 for Fe (original parameters),*gatom*=8 for Fe (modified parameters in erratum). Subtoutine**FS**was coded by Ja,es Elliott in April 2009.*GA population offspring generations*: specifies optimisation using a ``Lamarckian'' genetic algorithm[7] instead of Monte Carlo. If*STEPS*is defined, each new member of the population is optimised with a basin-hopping Monte Carlo search. The search will end when the number of*generations*has been exhausted or when solution specified by the*TARGET*keyword has been reached. Currently, this is only implemented for the*BLN*model protein and clusters. See §3.2 for more details.*GABHINCR increment*: specifies the use of a hybrid GA/basin-hopping algorithm with a variable length of basin-hopping search. The*increment*defines the number of extra basin-hopping steps to perform in each generation. This does not have to be an integer (e.g.*increment = 0.5*increases the number of basin-hopping steps by one after every other generation).*GACROSS n*: specifies*n*-point crossover for genetic algorithm mating operations. Permitted values for*n*are 1 and 2 (default = 1).*GADUMPPOP*: dump genomes of entire population after every generation.*GADUPPRED ethresh*: sets the energy threshold for the*GA*duplicate predator. If two structures differ by less than*ethresh*, they are marked as duplicates and the least stable one is removed from the population.*GAEPOCH ethresh save DUMP*: specifies the use of a new epoch operator to restart*GA*searches that have converged. If the mean energy of the population decreases by less than*ethresh*in one generation, a new population of random solutions is generated and a new epoch begins. Optionally, the best*save*solutions are carried over from one epoch to the next. Adding the optional*DUMP*statement prints the conents of the population to a file`epoch.n`at the end of each epoch.*GAINITCHAIN*: random structures at the start of an epoch in a*GA*search will be generated as a sequence continuous chain. If no*GAINIT...*option is specified, this will be chosen for*BLN*proteins.*GAINITSPHERE radius*: random structures at the start of an epoch in a*GA*search will be generated as points inside a sphere. If no*GAINIT...*keyword is specified, this will be chosen for clusters. The default*radius*is 3.0.*GAMUTRATE mutrate*: sets the mutation rate for*GA*searches. Default=0.1.*GASELROUL tournsize*: specifies the roulette wheel method to select parents for mating in*GA*searches. The probabilities for the roulette wheel are generated using a tanh fitness function.*GASELTOURN tournsize*: specifies the tournament method to select parents for mating in*GA*searches. Default*tournsize=3*.*GATWIN*: allow twinning moves for GA.*GBD kappa kappaprime mu nu sigma0 epsilon0*: calls a finite system of discoids interacting via a modified Gay-Berne pair potential due to Bates and Luckhurst [12].*GBH*: parallelised generalised basin hopping*GCBH mu nmax int relax prob*: specifies grand canonical basin-hopping.*mu*is the chemical potential,*nmax*is the maximum number of atoms,*int*is the interval between changes in the number of atoms,*relax*is the block size for relaxation with conventional BH steps,*prob*is the probability of increasing the number of atoms by one, and*1-prob*is the probability of removing an atom. The grand canonical accept/reject is based on the lowest potential obtained within a Markov chain of blocks, to allow the system to relax when the number of atoms increases or decreases. The atom removed is currently programmed to be the one that is most weakly bound, so this pair energy must be known. A new atom is added two distance units outside the current cluster defined by the atom furthest from the centre of coordinates. In both cases an initial quench is performed immediately, and the attempt is rejected if this quench is unsuccessful. Some declarations are based on*nmax*, while locally dynamic allocations for subroutines can use the current number of atoms. If*FEBH*is specified then the potential is based on the exponential factor and the partition function (including rotation if*USEROT*is used). Otherwise, the test is based on the potential defined by .*GEOMDIFFTOL diff*: tolerance on distance between two structures to be counted as identical.*GETCNSIZE tmin tmax tinc mumin mumax muinc maxmin*: for use with*CNBH*. Find the size corresponding to the estimated critical nucleus over a grid of temperature and chemical potential values.*tmin, tmax, tinc*are the minimum, maximum and temperature increment,*mumin, mumax, muinc*are the minimum, maximum and chemical potential increment.*maxmin*is the maximum number of minima to use in the superposition partition function for each size. Minima are taken in the order they are found in`min.data`.*GLJ n1 n2 n3 etc.*: specifies general Lennard-Jones potential for any number of differ LJ species. The and parameters for all the different species should be specified as the lower diagonal blocks of the corresponding matrices on the following lines. For example, to specify a 13-atom cluster with three different species: GLJ 6 4 3 1.0 1.1 1.2 1.2 1.3 1.4 1.0 1.5 1.6 1.7 1.8 1.9*GLJY alpha A xi*: specifies a combination of generalised Lennard-Jones and Yukawa potentials for colloidal systems. The potential is given by in reduced units with .*GROUND*: when combined with keywords*NEON*or*ARGON*uses an accurate (Aziz) potential to model the ground state neutral cluster.*GROUPROTATION (freq) (scalemode) (offset)*: specifies group rotation moves for groups of atoms defined in atomgroups.*freq*(optional) specified the frequency with which these moves should be made. The default, 1, specified group rotations be made every 1 steps.*scalemode*(optional) can be used to determine how the GROUPROTATION moves are scales to attempt to achieve the desired acceptance ratio. There are 4 options for*scalemode*-*SCALENONE*(default): do no scaling,*SCALEPROB*: scale the group selection probabilities,*SCALEROT*: scale the rotation amplitudes and*SCALEBOTH*: scale both selection probabilities and rotation amplitudes.*offset*(optional) can be used for systems with consistant ligand or cofactors to allow the ligand/cofactor group numbering to be system independant. For example, if there are 3500 atoms in a protein, and the ligand starts at atom 3501, setting*offset*to 3500 means that the GROUP in atomgroups numbering starts at 1 again. The default*offset*is 0. Currently this is only usable with*AMBER9*and*CHARMM*.The atomgroups file is formatted as follows:

*GROUP name bondatom1 bondatom2 groupsize rotationscalefactor probselect**groupatom1**groupatom2**groupatom3*...

The group rotation axis is defined by the vector from

*bondatom1*->*bondatom2*, and the rotation is scaled by*rotationscalefactor*.Here is an example atomgroups file containing two groups:

GROUP OME 6 5 4 1.0 0.8

1

2

3

4

GROUP CH2OH 23 25 4 1.0 0.8

26

27

28

29

*QUIETGROUPROT*: suppresses output from group rotation about which angles were changed.*GTHOMSON type param1 param2 param3 param4*: the system will be constrained to a curved surface. The type of surface is specified by*type*as follows:1 A cylinder, with height

*param1*and radius*param2*.2 A catenoid

3 An unduloid

4 An unduloid

5 A sphere, with radius

*param1*.6 A Möbius strip, with radius

*param1*and width*param2*.*GTHOMSONPOT type*: specifies the potential to use with the surface described by the*GTHOMSON*keyword. The values of*type*give the following behaviours:1 A Coulomb potential, with all particles having a charge of 1.

2 A potential.

3 A Yukawa potential, with screening length

*.*4 A Lennard-Jones potential, with characteristic distance

*and a well depth of 1.*5 A repulsive Lennard-Jones ( ) potential, with characteristic distance

*.*6 A Morse potential, with characteristic distance

*and range parameter**.**GUIDE guidecut*: specifies the RMS force below which the real potential is used rather than a guiding potential. The systems affected are*CPMD*and*WELCH*, which are guided by*AMBER*and*TOSI*, respectively, and also*PACHECO*, where the Axilrod-Teller contribution is only included when the RMS force falls below*guidecut*. Default*guidecut*=0.0001. New guided potentials are*ZETT1*and*ZETT2*(guided by Morse with ) and*NATB*(guided by*GUPTAT*). Parameters for the guiding potential must also be specified in`data`.*GUPTA gatom*: specifies a Gupta potential using parameters from Cleri and Rosato,*Phys. Rev. B*,**48**, 22 (1993).*gatom=1*for Ni,*gatom=2*for Cu,*gatom=3*for Rh,*gatom=4*for Pd,*gatom=5*for Ag,*gatom=6*for Ir,*gatom=7*for Pt,*gatom=8*for Au,*gatom=9*for Al,*gatom=10*for Pb,*gatom=11*for Ti type 1,*gatom=12*for Ti type 2,*gatom=13*for Zr type 1,*gatom=14*for Zr type 2,*gatom=15*for Co,*gatom=16*for Cd type 1,*gatom=17*for Cd type 2,*gatom=18*for Zn,*gatom=19*for Mg,*gatom=20*for V,*gatom=21*for Na,*gatom=22*for Sr (Wang and Blaisten-Barojas,*J. Chem. Phys.*,**115**, 3640 (2001)),*gatom=22*for Au as used by Garzon et al. The**Gupta**subroutine was recoded more efficiently by James Elliott in April 2009.*HBONDLIGAND (ligandresn)*: used with the*HBONDMATRIX*keyword. When specified, groups are defined only by the hydrogen-bonds between the ligand and protein only - not between sidechains. The optional arguement*ligandresn*specifies which line in the*residuefile*corresponds to the ligand. The default is to assume it is the last line of the file. This keyword must be specified after*HBONDMATRIX*in the data file.*HBONDMATRIX donoracceptorfile residuefile mode*: used with the*AMBER*keyword to focus GMIN sampling on the diversity of ligand binding-modes in a protein/ligand system.*donoracceptorfile*should contain the AMBER ptraj definitions of the hydrogen-bond donor and acceptor atoms for your system as described in the AMBER Tools manual (see Google).*residuefile*should contain the list of residue numbers (one per line) that are involved in binding. When you have no specific information, this can just mean those in close proximity to the binding site.*mode*is an optional arguement, which defaults to ACCEPT. If REJECT is used instead,*HBONDMATRIX*will instead restrict sampling to the binding mode identified after the initial quench. This can be used to optimise a single binding mode.*HBONDSOFTCUT dloose dtight aloose atight*: used with*HBONDMATRIX*to specify a custom cutoff window for the hydrogen-bond analysis used by the*HBONDMATRIX*keyword to group structures. The default values for the four parameters are 3.05, 2.95, 115.0 and 120.0. It should be noted that the actual angles used in the analysis are*aloose*and*atight*. This is why the looser angle cutoff is actually numerically smaller.*HYBRIDMIN rigidconv*: enables hybrid rigid body/all-atom minimisation when using*RIGIDINIT*.*rigidconv*is the RMS force convergence criterion for the rigid body minimisation. Once converged, an all-atom minimisation begins using the convergence specified in*SLOPPYCONV*. The final quenches are done atomistically.*INTMIN*: used with*CHARMM*keyword to specify minimisation in internal coordinates. This generally appears to be slower than using Cartesian coordinates.*INVERTP*: specifies the inverted potential. The energy and all derivatives are multiplied by . This converts searches for the highest index saddles into minimisation. However, it is only likely to work for bounded potentials.*JC*: Specifies Murrell's two- plus three-body potential.[13,14,15,16,17] A file`JMparams`must exist in the current directory containing the parameters and . An optional cutoff parameter can also be provided at the end of the`JMparams`file. Subroutines used:**jmec**,**jm2c**,**jm3c**.*JUMPMOVE np1 np2 int*: specify J-walking type attempts between parallel runs*np2*and*np1*at intervals of*int*steps.*LB2*specifies the potential[18,19,20](1)

where and are set to unity.*LFLIPS n m kT (mfac)*: for every*n*th step in the main basin-hopping sequence perform a subsequence of*m*steps with flip moves only. This subsequence constitutes an independent block of semi-grand canonical basin-hopping at a given*kT*, with the total number of atoms fixed but the relative population of constituent species allowed to vary. In every instance the subsequence starts with the specified value of*kT*, which is then multiplied by the (optional) parameter*mfac*on each of the*m*successive steps. (Default:*mfac = 1*.) The keyword*SEMIGRAND_MU*can be used to impose non-zero semi-grand chemical potentials (with respect to the first species).*LFLIPS_RESET*: at the start of every subsequence of flips, the stoichiometry will be reset to the value inferred from the keyword specifying the multicomponent potential. The atomic labels will be reassigned randomly.*LIGMOVE ligrotscale ligcartstep ligtransstep ligmovefreq*: used with*AMBER9*and*MOVABLEATOMS*. Specifies ligand only rotation, cartesian perturbation and translation. The ligand is defined by atom index in the file 'movableatoms'. Setting*ligrotscale*less than 1.0 limits the ammount of rotation possible - this may be required to prevent cold fusion with non-spherical ligands.*ligcartstep*and*ligtransstep*define the maximum size (in angstroms) of the random cartesian perturbations and rigid body translation applied to the ligand respectively.*ligmovefreq*can be set to greater than 1 to prevent ligand moves being applied every step i.e.*ligmovefreq = 2*for every other step. All ligand moves are applied AFTER any MD if*AMBERMDMOVES*is on to prevent the MD exploding.*LJADD*: specifies an addressable LJ potential. A data file`epsilon`is required specifying the well depth parameter for all pairs of atoms, one per line. Choosing values according to nearest neighbours in a reference geometry can bias the system towards that configuration.*LJADD2 n*: specifies an addressable LJ potential for multiple copies of an -particle cluster. The data file`epsilon`is required with entries, one per line. These well depth parameters are then applied modulo . For particles with the same address, only the repulsive part of the LJ potential is used.*LJAT scale*: specifies the Lennard-Jones plus Axilrod-Teller potential for a reduced triple-dipole strength of . Provided mostly as a guiding function for*DFTBC*.*rescale*is the coordinate rescaling factor from the LJAT potential to DFTB, default value 2.424.*LJCOUL nc f*specifies a cluster of Lennard-Jones particles in which the first*nc*particles carry identical reduced charges*in addition to the Lennard-Jones interaction. The parameter**f*specifies what fraction of the Monte Carlo steps should be swaps between the positions of a charged and a neutral particle, rather than a conventional step. is the temperature to be used in the acceptance criterion for swap moves, overriding that specified using the*TEMPERATURE*keyword. Generally, a lower temperature is more effective at finding the lowest-energy permutation of charges. The default value of is zero. The reduced charge is related to the actual charge by , where and are the Lennard-Jones well depth and length parameter respectively. This way, the reduced energy of two charges is , where is the reduced distance bdetween the charges.*LJGAUSS mode rcut params*specifies that the Lennard-Jones Gauss double well potential should be used. The Lennard-Jones potential has an energy minimum of 1 and a minimum at distance 1. The relative weight of the Gaussian potential is and the Gaussian peak is at distance . The width of the Gaussian is controlled by . The Stoddard-Ford procedure is used to make the potential and its first derivatives go smoothly to zero at*rcut*.*mode*can be either 0, 1, 2 or 3. mode 0 specifies the normal potential, and can be either a cluster or with periodic boundary conditions with an orthogonal unit cell using the PERIODIC keyword. mode 1 or 2 requires periodic boundary conditions. The PERIODIC keyword must be used, but the unit cell parameters from it will be ignored. Instead, the last line of the coords file will be interpreted as the unit cell length parameters and will be optimised. Additionally, for*mode*2, the second last line of the coords file be interpreted as unit cell angle parameters for a triclinic unit cell, and optimised. Since there are combinations of unit cell angles that are physically impossible, steps will be rejected if such combinations are detected. In mode 3, as well as the cell being optimised, potential parameters specified by params (an integer between 1 and 7) will also be optimised. If the 1 bit of params is set, will be optimised, if the 2 bit is set, will be optimised, and if the 4 bit is set, will be optimised.*LOCALSAMPLE abthresh acthresh*: Keyword currently under construction! For three groups of atoms defined in movableatoms (A,B,C), a step is quenched when the centre of coordinates of A->B is less than*abthresh*AND A->C is less than*acthresh*. If this condition is broken AFTER the quench, it is automatically rejected.*LPERMDIST n thresh cut orbittol*: provides the preferred local permutational alignment procedure.*n*is the maximum number of extra atoms to include in running**minperm**for each permutable group (default 11, a value that may be needed to treat phenylalanine), rather than treating the whole system at the same time, as for*PERMDIST*. The extra atoms that define the neighbourhood of the permutable group are added one at a time in order of their distance from the centre of coordinates of the group, averaged over the start and finish geometries. If the optimal aligned distance is greater than*thresh*(default value 0.2) then the atom is not included in the neighbour list. This procedure continues until there are*n*atoms in the neighbour list, or no more atoms within the cutoff distance*cut*, default 10.0. The parameter*orbittol*is the distance tolerance for assigning atoms to orbits in the**myorient**standard orientation routine, default value 0.001. This keyword requires the auxiliary file`perm.allow`to specify permutable atoms, otherwise all atoms are assumed to be permutable. The absence of a`perm.allow`file is considered a mistake for*CHARMM*runs.*LSWAPS n m kT (mfac)*: for every*n*th step in the main basin-hopping sequence perform a subsequence of*m*steps with exchange moves only. The keyword is intended for homotop optimisation at regular intervals for a given*kT*. In every instance the subsequence starts with the specified value of*kT*, and this value is multiplied by the (optional) parameter*mfac*on each of the*m*successive steps. (Default:*mfac = 1*.)- MAKEOLIGO START
dmin dmax SCONLY
specifies the oligomer generation procedure. Here, the sample input follows for the generation of a dimer.
The argument START specifies that a new oligomer is to be generated.
The second and third arguments determine how many peptide chains are fixed (
*nfix*) and relocatable (*nmove*), respectively. The input geometry has to be provided in such a form that all fixed peptide chains come first, followed by the peptide chains, which are set to new positions during the oligomer generation procedure. The secondary structures of the relocatable peptides are determined via the input geometry. The following 4*nmove*arguments specify the first and last atom for each of the relocatable peptide chains, and the minimum and maximum angle between which the relocatable peptide in question is to be positioned in the -plane: with . The next two arguments determine the minimum and maximum distances,*dmin*and*dmax*, which define the boundaries for the relocation of the peptide chains with respect to the centre of mass of the fixed part of the input structure. The effect of the last argument SCONLY is that during the subsequent optimisation of the oligomer only the dihedral angles of the sidechains are perturbed. If this argument is not present, the backbone dihedrals are also changed. The MAKEOLIGO keyword also affects the rigid body translation and rotation during the subsequent optimisation. The translation is only performed in the -plane. The rotation can be performed either around the -axis only or in the in the full three-dimensional space, depending on whether the first argument is START (as in this example) or INITROT. The arguments following INITROT are identical to those following START. *MAXBFGS max*:*max*is the largest permitted LBFGS step.*MAXERISE maxez*: specifies the largest rise in energy permitted during an LBFGS minimisation. MAXERISE must to be large enough for discontinuities encountered during quenches to be ignored, or the quench may fail. The default is , or , for periodic boundary conditions, where discontinuities can arrise due to multiple images.*MAXIT maxit maxit2*:*maxit*and*maxit2*are integers specifying the maximum number of iterations allowed in the conjugate gradient quenches.*maxit*applies to the `sloppy' quenches of the basin-hopping run and*maxit2*to the final quenches that are used to produce the output in file`lowest`.*MD nsteps (nwait nfreq)*: Perform*nsteps*molecular dynamics (MD) time steps instead of basin-hopping. Current implementation works only for Cartesian coordinates (not the rigid-body framework), and the atomic positions are dumped to`dump.1.xyz`every*nfreq*steps after the first*nwait*steps, with*nwait = nsteps*by default (i.e. no dumping). Time-stepping for each coordinate is carried out using the velocity Verlet scheme with a Langevin thermostat:

where , and are the coordinate, velocity and acceleration, respectively, with the subscript specifying the time instance; is the time step (see MDPARAMS); is the atomic mass (see SPECMASS); is a damping parameter (see MDPARAMS); and and are (independent) random numbers from the normal distribution with mean 0 and variance . The instantaneous acceleration/force is derived from the potential; the initial coordinates are read from the`coords`file; the velocities are initialised randomly using the Maxwell distribution, with set by the TEMPERATURE keyword and net translation and rotation subtracted.*MDPARAMS tstep gamma*: Specifies the timestep (tstep = 0.002 by default, with units determined by the potential) and Langevin damping parameter (gamma = 0.0 by default, with units of inverse time). The default values are tailored for microcanonical MD of atoms with unit mass. For canonical MD one should choose gamma > 0 such that 0 < gamma*tstep < 1, e.g. gamma of around 10 is adequate for the default time step.*MERGEDB dir*: merge the`min.data`,`points.min`,`min.frqs`files from directory*dir*with those in the current directory. Common stationary points are identified and not repeated. Merged results are created corresponding to all the above files.*MGGLUE*: specifies a glue potential for magnesium*MLOWEST*: Like TARGET. Accepts multiple target energies and will stop upon hitting *all* targets as opposed to *any* target.*MORSE rho*: specifies a Morse potential with range parameter*rho*.[21,22,23]*MPI*: specifies an MPI parallel job. (only available if the source is compiled with MPI enabled).*MGUPTA nspecs A_11 p_11 q_11 xi_11 r0_11*: specifies a multicomponent Gupta potential for*nspecs*distinct metallic species. If*nspecs = 1*then this single line is sufficient. The model parameters*A_11*,*p_11*,*q_11*,*xi_11*and*r0_11*have the same meaning as for the keyword*BGUPTAT*. If*nspecs 1*, then more subsequent lines of the form*MGUPTA (n_I) A_IJ p_IJ q_IJ xi_IJ r0_IJ*must be supplied for all the remaining*I,J [1,nspecs]*in ascending order with . Note that*n_I*is expected only when , with*n_I*specifying the number of atoms for each species*I 1*. The value for*n_1 (= n_A)*is inferred from the knowledge of the total number of atoms (*NATOMS*). For example, a ternary system ABC (*N = NATOMS*) should be specified in six consecutive lines:*MGUPTA*3 *A_AA**p_AA**q_AA**xi_AA**r0_AA**MGUPTA**A_AB**p_AB**q_AB**xi_AB**r0_AB**MGUPTA**A_AC**p_AC**q_AC**xi_AC**r0_AC**MGUPTA**k**A_BB**p_BB**q_BB**xi_BB**r0_BB**MGUPTA**A_BC**p_BC**q_BC**xi_BC**r0_BC**MGUPTA**k**A_CC**p_CC**q_CC**xi_CC**r0_CC**MIE_FIELD filename Rc Bx By Bz*: specifies a fixed substrate from superposition of Mie-type central force fields, each defined by*filename*. The expected file format is:

where and are given for each species (e.g. for nanoalloys). Mie field(s) can be smoothly truncated using the optional cut-off parameter Rc, which will trigger the usual Stoddard and Ford procedure:*MIN_ZERO_SEP separation attempts*: when used in combination with the*FEBH*keyword, this will tighten the rms force convergence thresholds until where is the value given by*separation*. If*attempts*is specified, the GMIN run will terminate if the separation is not achieved within the specified number of attempts. This is usually indicative of a problem with the potential or eigenvalue calculation.*MLJ nspecs eps_11 sig_11*: specifies a multicomponent Lennard-Jones potential for*nspecs*distinct species. If*nspecs = 1*then this single line is sufficient, and it ought to yield the same results as the standard Lennard-Jones. Extension to*nspecs 1*is analogous to the*MGUPTA*keyword, and it differs from the input format expected by the*GLJ*keyword. Note that, although*GLJ*and*MLJ*link to different implementations of the general multicomponent Lennard-Jones, they ought to yield the same results.*MLPB3 inhidden out data*specifies a multi-layer perceptron neural network with*in*input nodes,*hidden*hidden nodes,*out*output nodes, regularisation constant and bias nodes for the hidden and output sums. The activation function for the hidden layer is hyperbolic tan. The activation function for the output layer is just the sum, so the bias potential here does nothing. The outputs are normalised softmax probabilities and the L2 regularisation term (to prevent overfitting) is:(2)

where is the class label for data point specified by the training set, and is a constant. The regularization is performed on all parameter degrees of freedom except for the bias nodes. The number of variables is*hidden(in+out)+1*. There is another keyword*MLP3*, which is exactly the same without the bias nodes.*MSC nspecs nn11 mm11 sig11 sceps11 scc1*: specifies a multicomponent Sutton-Chen potential for*nspecs*distinct metallic species. If*nspecs = 1*then this single line is sufficient, and it can be used in conjunction with keywords*PERIODIC*and*CUTOFF*. The parameters*nn11*,*mm11*,*sig11*,*sceps11*and*scc11*have the same meaning as for the keyword*SC*. If a cutoff has been specified, then the potential will be smoothly truncated by a generalised Stoddard and Ford procedure, which ensures the energy and its first derivatives remain continuous. If*nspecs 1*, then more subsequent lines of the form*MSC (ntypeI) nnIJ mmIJ sigIJ scepsIJ (sccI)*must be supplied for all the remaining*I,J [1,nspecs]*in ascending order with . The parameters*ntypeI*and*sccI*are expected only when , with*ntypeI*specifying the number of atoms for each species*I 1*. The value for*ntype1 (= ntypeA)*is inferred from the knowledge of the total number of atoms (*NATOMS*). For example, a ternary system ABC (*N = NATOMS*) should be specified in six consecutive lines:*MSC*3 *nnAA**mmAA**sigAA**scepsAA**sccA**MSC**nnAB**mmAB**sigAB**scepsAB**MSC**nnAC**mmAC**sigAC**scepsAC**MSC**k**nnBB**mmBB**sigBB**scepsBB**sccB**MSC**nnBC**mmBC**sigBC**scepsBC**MSC**l**nnCC**mmCC**sigCC**scepsCC**sccC**MSORIG*: specifies a particular tight-binding potential for silicon.*MSTRANS*: specifies an alternative tight-binding potential for silicon.*MULLERBROWN*: specifies the 2D Muller-Brown potential.*MULTIPOT*: Use the flexible multiple potential scheme to define your system. Different atoms can interact via different types of potential and a particular atom can be associated with more than one type of potential. Detailed instructions to use this scheme are given as comments in`multipot.f90`,`pairwise_potentials.f90`and`isotropic_potentials.f90`.In theory, any subroutine with the correct signature can be used as a potential function. Only the potentials in

`pairwise_potentials.f90`and`isotropic_potentials.f90`have been tested. At the time of writing, these are the LJ, WCA and harmonic-spring potentials.`pairwise_potentials.f90`contains functions which are called for a pair of atoms at a time (e.g. harmonic springs).`isotropic_potentials.f90`contains functions which require coordinates of all the atoms involved in the interaction. Although LJ and WCA are pairwise potentials, it is more efficient to treat them as isotropic and loop over interacting pairs in the function call rather than to call pairwise_lj for every pair of atoms ( function calls give a large performance overhead).`pairwise_potentials.f90`and`isotropic_potentials.f90`contain generic functions for calculating the first and second derivatives of isotropic pairwise potential functions. Detailed instructions are found in the source code.An input file

`multipotconfig`is used to specify which potential functions are to be used and which atoms use each potential. For each type of potential in the system,`multipotconfig`should contain the following:

*POT**POTTYPE n scale nparams**[params]*followed by a list of atom indices which will use this potential (the format of the list will depend on the particular potential).

*POTTYPE*is a string identifier for the type of potential being used,*n*is the number of atoms using this potential and*scale*is the energy unit for this potential (which should be set to 1.0 for at least one potential).*nparams*is the number of potential-specific parameters which are required, and*[params]*is a list of these parameters.Be aware that using

*MULTIPOT*will give a slight performance hit, because of the several function calls and bookkeeping that is associated with each call to*POTENTIAL*. This scheme is intended for playing around with composite potentials, for systems which are small enough that performance is not a big issue, or for systems involving many different potential functions which will be much too fiddly to hard-code a single subroutine.*MULTIPERM*: instead of basin-hopping, systematically span the permutation space of the multiset containing particle labels. Uses a more general algorithm than*ENPERMS*.*MULTIPLICITY xmul*: specifies the multiplicity of the electronic state in*DFTB*calculations.*MWPOT*: calls a Stillinger-Weber type potential with parameters appropriate for water[24].*NATB*: specifies the sodium tight-binding potential of Calvo and Spiegelmann. This potential can be guided by also specifying*GUPTA 21*in the`data`file.*NCAP*: calls the capsid model [25], consisting of pentagonal building blocks.*NEON*: introduces a diatomics-in-molecules calculation for a neutral, cationic or electronically excited neon cluster. See also*GROUND*,*PLUS*,*TWOPLUS*and*STAR*.*NEWJUMP prob*: for (serial) `parallel' runs specifies a jump probability between runs (parallel tempering) of*prob*. See the*BHPT*keyword for a better alternative.*NEWRESTART nrelax nhs MD newrestemp*: reseed runs if the energy does not decrease within*nrelax*steps.*nhs*is the number of hard sphere moves used to produce the new starting configuration. If*nhs=0*(the default) then the geometry is changed by reseeding. If*MD*is present, then a short AMBER or CHARMM MD run is performed at temperature*newrestemp*(specified in K, default 1000K) to generate the new configuration. If the `F' argument appears for*AVOID*then*NEWRESTART*will not reseed.*NEWTSALLIS q*: specifies that steps are accepted/rejected using Tsallis statistics with the given value of*q*, rather than the usual Boltzmann condition. This version is slightly different from "TSALLIS" keyword.*NOCHIRALCHECKS*: disables checks for inversion of CA atoms and chiral side-chains for ILE and THR.*NOCISTRANSCHECKS*: disables checks for isomerisation of the peptide bond. This is equivalent to using the*CISTRANS*keyword.*NOCISTRANS minomega*: set on by default with a threshold*minomega*of 150 degrees. If an amide bond is deformed to a angle below the specified threshold, the structure is discarded. i.e. with*minomega*.*minomega*defaults to 150 degrees. For proline every is allowed. To enable cis-trans isomerisation, the*CISTRANS*keyword should be used.*NOCISTRANSDNA minomega*: should be specified when working with DNA in AMBER to ensure the correct bonds are checked. As above, the deformation threshold*minomega*can be set. It is defaulted to 150 degrees.*NOCISTRANSRNA minomega*: should be specified when working with RNA in AMBER to ensure the correct bonds are checked. As above, the deformation threshold*minomega*can be set. It is defaulted to 150 degrees.*NOFREEZE*: don't freeze the core atoms when doing the initial geometry optimisations in a run where*SEED*is specified.*NOGETROT*: do not include the rotational partition function; for use with*FEBH*and*CNBH*.*NOGETVIB*: do not include the vibrational partition function; for use with*FEBH*and*CNBH*.*NOGETTRANS*: do not include the factor in the translational part of the partition function; for use with*FEBH*and*CNBH*.*NOGETSYM*: do not include the factor in the partition function for use with*FEBH*and*CNBH*.*NOINVERSION*: turns off inversion of structures for distance metric in**minpermdist**.*NOPHIPSI*: used with the*CHARMM*keyword to specify twisting of sidechain dihedrals only.*NOPOINTS*: if*USEMINDATA*is specified then a`points.min`file is created with entries corresponding to`min.data`unless*NOPOINTS*is set. The points file is not used for identifying minima; instead we check the energy and the principal moments of inertia.*NORESET*: by default the configuration point is set to that of the quench minimum in the Markov chain during a basin-hopping simulation. This keyword turns off the resetting so that the geometry varies continuously.*NOTE*: the rest of the line is ignored.*NPAH n*: calls a finite system of polycyclic aromatic hydrocarbons (PAH) interacting via Williams' potential [26]. The PAH ID*n*defines the PAH molecule: 1 for coronene, 2 for pyrene, 3 for benzene.*NRELAXRIGID MinR MinA*: Minimizations will use rigid body coordinates for MinR steps and then atomistic coordinates for MinA steps. This is to be used with*RIGIDINIT*keyword.*NTIP n*: calls a member of TIP family of potentials for water molecules within a rigid-body framework. . : TIPS water; : TIPS2 water; : TIP3P water; : TIP4P water; and : TIP5P water.*ODIHE*: order parameter--requires documentation.*OEINT*: interaction energy between 2 peptides will be used as an order parameter--requires further documentation.*OHCELL*: allow point group operations for a cubic supercell in subroutine`minpermdist.f90`permutational distance minimisation.*OPEP option*: specifies the use of the OPEP poetential,*option*is either PROTEIN or RNA. The following additional files are needed: conf_initiale.pdb, which contains the starting configuration and the atom information, OPEP_params, which can contain additional settings for example for debugging, ichain.dat, scale.dat, cutoffs.dat, parametres.top and parametres.list, which are the generic OPEP files.*OPP mode rcut xplor k params k_lower k_upper*specifies that the Oscillating Pair Potential potential should be used. This potential can have several wells, depending on the value of k, a frequency parameter, and , a phase parameter. The XPLOR smoothing function is used to make the potential and its first derivatives go smoothly to zero at*rcut*, with the smoothing beginning at xplor (which must be less than rcut).*mode*can be either 0, 1, 2 or 3. mode 0 specifies the normal potential, and can be either a cluster or with periodic boundary conditions with an orthogonal unit cell using the PERIODIC keyword. mode 1 or 2 requires periodic boundary conditions. The PERIODIC keyword must be used, but the unit cell parameters from it will be ignored. Instead, the second last line of the coords file will be interpreted as unit cell angles and the last line as unit cell lengths for a triclinic cell and will be optimised. Since there are combinations of unit cell angles that are physically impossible, steps will be rejected if such combinations are detected. In mode 2, as well as the cell being optimised, potential parameters specified by params (an integer between 1 and 3) will also be optimised. If the lowest bit of params is set, k will be optimised, and if the second bit is set, will be optimised. In mode 3, potential parameters will be optimised as for mode 2, but there are no periodic boundary conditions. For mode 2 and 3, the lower and upper bounds for k can be specified with k_lower and k_upper. If k steps outside these bounds, a harmonic repulsion will be turned on to push k back towards the range.*ORBITALS*: orbital localisation rotation potential.*ORGYR*: radius of gyration will be calculated as an order parameter--requires further documentation.*OSASA*: order parameter--requires documentation.*P46*: specifies a 46-bead three-colour model polypeptide. See also the*BLN*keyword, which implements this potential in a more general way and uses unit bond lengths.*PACHECO*: specifies the intermolecular Pacheco-Ramelho potential for C. The Axilrod-Teller contribution, specified with the*AXTELL*keyword, is included when the RMS force falls below the value entered with*GUIDECUT*.*PAH*: specifies a polycyclic aromatic hydrocarbon potential.*PAHA n*: calls a finite system of polycyclic aromatic hydrocarbons (PAH) interacting via a general anisotropic potential developed from first principles [9]. The PAH ID*n*defines the PAH molecule: 1 for benzene, 2 for naphthalene, 3 for anthracene, and 4 for pyrene.*PAHAGENRIGID n*: calls a finite system of polycyclic aromatic hydrocarbons (PAH) interacting via a general anisotropic potential developed from first principles [9]. This potential has been adapted to the GENRIGID framework for rigid bodies (also use the*RIGIDINIT*keyword). The PAH ID*n*defines the PAH molecule: 1 for benzene, 2 for napthalene, 3 for anthracene, and 4 for pyrene.*PAIRDIST pair1a pair1b pair2a pair2b...*: enables tracking of the distances between pairs of atoms during a GMIN run. Atom pairs may be specified in the keyword definition as shown, or in the file`pairdist`with a pair of atoms on each line. The pair distances are calculated after each quench and printed in`pairdists`.*PAP npatch alpha s cosdel epsilon*: specifies a patch anti-patch potential. Each body consists of a Lennard-Jones core, range parameter*alpha*, with*npatch*patches and*npatch*anti-patches. The patch anti-patch attraction has a range specified by*s*, a width specified by*cosdel*and a strength specified by*epsilon*. If*npatch*is set to zero, site information will be read in from the file`papsites.xyz`.*PARALLEL npar GMIN*:*npar*is the number of parallel runs within GMIN. If the word "GMIN" is present as the second argument, the calculation will proceed until the same lowest energy is recorded in each trajectory.*PBGLUE*: specifies a glue potential for lead.*PERCOLATE dist comp cutoff*: specifies that particles are prevented from evaporating using a system based on maintaining a percolating graph of particles, rather than using a container, with*dist*as the maximum distance at which particles are considered to be connected. An optional harmonic compression potential can be specified with force constant*comp*, to be turned off below RMS force*cutoff*. Currently, the step size is limited to*dist*squared.*PERIODIC boxlx boxly boxlz alpha beta gamma*: specifies periodic boundary conditions for potentials which understand such a directive. The three variables*boxlx, boxly, boxlz*are the box lengths. If only one box length is given, the others are set to the same value to give a cube. The three variables*alpha, beta, gamma*are the box angles in radians. If the box angles are not given, the box is taken to be orthorhombic.*PERMDIST x*: minimise distances between the coordinates in files`coords`and the fixed coordinates in file`finish`with respect to permutational isomerisation. Requires the auxiliary file`perm.allow`to specify permutable atoms, otherwise all atoms are assumed to be permutable. The absence of a`perm.allow`file is considered a mistake for*CHARMM*runs. The parameter*x*is the distance tolerance for assigning atoms to orbits in the**myorient**standard orientation routine, default value 0.001. If*x*is too small it is possible for permutational isomers to be missed, however, if*x*is too large then runs with the*AVOID*keyword can slow down by an order of magnitude.The first line of the

`perm.allow`file must contain an integer that specifies the number of primary groups of interchangeable atoms. The groups then follow, each one introduced by a line with two integers and that specify the number of permutable atoms in the primary group and the number of other sets of permutable atoms associated with the primary set. may be zero. Each secondary set of permutable atoms has members. The following line contains the indices of the permutable atoms in the primary set and then the indices of the atoms in each of the secondary sets, one set at a time.For the phenylalanine example illustrated we must allow three other pairs of atoms to exchange if we swap 7 and 8. Hence a suitable

`perm.allow`entry is 12 3

7 8 5 6 1 2 3 4 Here and : if we exchange 7 and 8 then we must also exchange 5 and 6, 1 and 2, and 3 and 4. There are two atoms in each of the three secondary sets, since we have specified 7 and 8 as the two primary atoms.

Here is an example

`perm.allow`file for a water trimer using the flexible*QTIP4PF*potential, where the energy is invariant to permutations of water molecules and to exchanges of hydrogens in the same molecule. However, hydrogens cannot exchange between different oxygens: 43 2

1 4 7 2 3 5 6 8 9

2 0

2 3

2 0

5 6

2 0

8 9 The first group of three oxygens has two atoms that must move with each oxygen, i.e. atoms 2 and 3 for oxygen 1, etc. Hydrogen permutations for each oxygen are allowed by the three following groups. This scheme allows atoms to appear in more than one group. There must be a group containing each complete set of permutations in order for permutation-inversion isomers to be recognised. The format is compatible with an older scheme, where only pair swaps were allowed for associated atoms, but now allows for more general permutations.

Scripts to generate allowed permutations automatically for CHARMM and AMBER are available from the group web site. It is essential to use symmetrised versions of the corresponding force fields!

*PERMINVOPT x*: minimise the distance between the geometries in`coords`and`finish`with respect to permutations, as well as overall translation, rotation, and inversion. See*PERMOPT*for distance optimisation without the inversion. To specify specific groups of permutable atoms a`perm.allow`file is needed, unless all atoms (or rigid bodies) are considered permutable. For rigid bodies the file`rbsymops`can be used to specify symmetry operations of each molecule, and the distance will then also be minimised with respect to internal symmetry operations. To minimise the Euclidean distance between two configurations with no permutations a`perm.allow`file with the single entry `0' can be used. The configurations are then aligned as if they were rigid bodies decorated with fixed sites. The parameter*x*is the distance tolerance for assigning atoms to orbits in the**myorient**standard orientation routine, default value 0.001. If*x*is too small it is possible for permutational isomers to be missed, however, if*x*is too large then runs with the*AVOID*keyword can slow down by an order of magnitude.*PERMOPT x*: minimise the distance between the geometries in`coords`and`finish`with respect to permutations, as well as overall translation and rotation, but not the inversion. To specify specific groups of permutable atoms a`perm.allow`file is needed, unless all atoms (or rigid bodies) are considered permutable. For rigid bodies the file`rbsymops`can be used to specify symmetry operations of each molecule, and the distance will then also be minimised with respect to internal symmetry operations. To minimise the Euclidean distance between two configurations with no permutations a`perm.allow`file with the single entry `0' can be used. The configurations are then aligned as if they were rigid bodies decorated with fixed sites. The parameter*x*is the distance tolerance for assigning atoms to orbits in the**myorient**standard orientation routine, default value 0.001. If*x*is too small it is possible for permutational isomers to be missed, however, if*x*is too large then runs with the*AVOID*keyword can slow down by an order of magnitude.*PLANCK h*: specifies the value of Planck's constant. This is used in calculating partition functions in*FEBH*and*CNBH*. SI units are needed for*TIP4PGR*and*AMBER12*. A value of the Planck constant in reduced LJ usits for a specific system is needed for intert gases with LJ.*PLUS*: when combined with keywords*NEON*or*ARGON*uses a diatomics-in-molecules potential for the singly charged cation.*POLYHEDRA overlap compress*the system is composed of convex polyhedra, with a harmonic repulsion of force constant*overlap*dependent on the distance by which a pair of polyhedra overlap with each other, and a harmonic attraction of force constant*compress*to bring the particles towards the origin. All polyhedra in the system are identical and their vertices are specified in the file`polyhedron_vertices.dat`. The first line of this file is the number of vertices, which must be at least 4, and the following lines give the coordinates of each vertex.*POWER ipow*:*ipow*is the initial power for shifts in the old line minimisation routine for conjugate gradient. LBFGS minimisation should be used instead.*PROJI*: turns on projection operator to enforce point group symmetry in**mylbfgs.f**. The geometry is projected after every proposed step.*PROJIH*: turns on projection operator to enforce point group symmetry in**mylbfgs.f**. The geometry is projected after every proposed step.*PRTFRQ n*: prints the energy every*n*steps; default is every step. Should now work for basin-hopping, basin-sampling and parallel tempering runs.*PRINT_PTGRP tol1 tol2 tol3*: Print point-group classification and order for each structure saved in the file`lowest`. The three tolerances are optional:*tol1*is a dimensionless tolerance for diagnosing degeneracies in (normalised!) principal moments of inertia,*tol2*is the distance tolerance used for detecting point-group symmetry operations, and*tol3*is a dimensionless tolerance used for testing whether a generated rotation matrix (representing a symmetry operation) is new. The default values are , and , respectively.*PRINT_MINDATA eigen_tol*: Print the energy, log product of (non-zero) Hessian eigenvalues, and the order of point group for each minimum in the file`lowest`, instead of the usual comment line. The optional real-valued parameter*eigen_tol*sets the tolerance for diagnosing negative (less than`-abs(eigen_tol)`) or zero Hessian eigenvalues. The default value is*eigen_tol = 0.001*. Note that if a negative eigenvalue is diagnosed or if the number of zero eigenvalues is unexpected, then the ``minimum'' will not be written to the file`lowest`.*PTMC histmin histmax ptemin ptemax pttmin pttmax exchprob nequil ptsteps nenrper hbins*: requests a standard parallel tempering MC run. This keyword also specifies the energy range for the histogram of quench energies,*histmin*to*histmax*, the energy range for the histogram of instantaneous configurations,*ptemin*to*ptemax*, the temperature range (*pttmin*and*pttmax*), the probability of attempting an exchange*exchprob*, the number of equilibration steps,*nequil*, the number of parallel tempering MC steps without quenching,*ptsteps*, the number of bins for the histogram of instantaneous potential energy,*nenrper*, and the number of bins for the histogram of quench energies,*hbins*. Should be used together with the*MPI*keyword. (This option is only available if the source is compiled with an MPI enabled.)*PTSTST npatch eps cosdel kappa*Specifies a patchy site-to-site potential, similar tp*PAP*but with Gaussian patches on the surface of the particle. The number of patches is determined by*npatch*.*eps*is the strength of the Gaussian patch attraction,*cosdel*is the effective range of the Gaussian and*kappa*is the Yukawa parameter for the core repulsion (currently unused as the core is Lennard-Jones rather than Yukawa).*PULL a1 a2 f*: apply a static force to the potential, equivalent to adding the term . Here and are the coordinates for atoms and , and specifies the force. This potential is designed to simulate a pulling experiment with static force where a molecule is pulled along the axis from atoms and .*PY sig0 eps0 [cutoff XYZ xbox ybox zbox]*: specifies a rigid-body multisite Paramonov-Yaliraki[27] potential with parameters and . Optional arguments are a cutoff distance in absolute units, a specification of which directions have periodic boundary conditions, and the size of the periodic box in units of the cutoff. The parameters for and setup of the rigid body, even if it is just one site, must be specified in a file`pysites.xyz`.There are two formats for

`pysites.xyz`: identical particles and n-ary mixtures. For identical particles, the format is:[number of sites in molecule] [blank line] site [x position] [y] [z] shapes [rep coeff] [att coeff] [a11] [a12] [a13] [a21] [a22] a[23] orient [p_x] [p_y] [p_z] ... site [x position] [y] [z] shapes [rep coeff] [att coeff] [a11] [a12] [a13] [a21] [a22] a[23] orient [p_x] [p_y] [p_z]

For an n-ary mixture,0 [the number zero] [arity] [blank line] [number fraction of this type of molecule] [number of sites in molecule] [normal site lines] ... [blank line] [second number fraction] [number of sites in second type] [normal site lines] ...

For example, for a single site molecule,1 site 0.0 0.0 0.0 shapes 1.0 1.0 0.5 0.5 0.2 0.5 0.5 0.2 orient 0.0 0.0 0.0

Or, for example, for two-to-one mixture of single sites and pairs,

0 2 0.66 1 site 0.0 0.0 0.0 shapes 1.0 1.0 0.5 0.5 0.2 0.5 0.5 0.2 orient 0.0 0.0 0.0 0.34 2 site 0.0 0.5 0.0 shapes 1.0 1.0 0.5 0.5 0.2 0.5 0.5 0.2 orient 0.0 0.2 0.0 site 0.0 -0.5 0.0 shapes 1.0 1.0 0.5 0.5 0.2 0.5 0.5 0.2 orient 0.0 -0.2 0.0

*QALCS qalcsmode cutoff*: perform Quench-Assisted Local Combinatorial Search to locate a biminimum for a multicomponent system. (More general than*HOMOREF*, which works only for binary systems.) The search comprises a sequence of quench-assisted atom swaps, where each step involves a sweep through the local neighbourhood structure induced by the ``interchange'' distance metric. There are many ways of doing this:*qalcsmode=0*specifies a slow steepest-descent-like search in permutation space; whereas modes 1 through 5 specify alternative schemes that are more efficient for larger systems. Modes 4 and 5 admit an additional (optional) integer parameter*cutoff*, which specifies that only the first*cutoff*entries in the sorted local neighbourhood are to be considered. The sorting is done by approximate swap gain.*QALCS_SURF*: specifies that QALCS should include surface vacancies as a separate species, akin to dynamic-lattice-search-type methods but relies on a different construction of surface vacancies. The scheme constitutes a deterministic way of refining the surface of a cluster within the QALCS framework, and it can be used with or without the*QALCS*keyword (for single- or multi-component clusters). Note that during the surface optimisation all particles are treated as being the same.*QMAX cgmax*:*cgmax*is the tolerance for the RMS force in the final set of quenches that are used to produce the output for file`lowest`. The default is*cgmax*, but the appropriate value depends upon the system in question.*TIGHTCONV*can be used instead.*QUAD*: requires documentation.*QUCENTRE*: sets the centre of coordinates to the origin (0,0,0) before each MC step is taken (so after each quench), but not during the minimisation itself unlike*CENTRE*.*RADIUS radius*: sets the radius of the container that prevents particles evaporating during quenches. If unset the program calculates an appropriate value based upon the volume per particle for close-packed material and the known pair equilibrium distance for the given potential. The formula employed is*RANDOMSEED*: specifies that the random number generator should be seeded with system time after each quench, allowing simple parallel use. Currently functional only for the CHARMM and AMBER potentials.*RANSEED i*: integer seed for the random number generator. The number actually used is mod(*i*,10000)+1.*RANDMULTIPERM n*: randomly permute atomic labels every*n*basin-hopping steps. Intended for use in conjunction with keyword*QALCS*.*RATIO stepratio tempratio*: adjusts stepsize and temperature independently.*stepratio*is the target fraction of steps that move into a different well. Identity of structures is determined by structural alignment; as such, the*PERMDIST*keyword and appropriate auxiliary files are required.*tempratio*is the target acceptance ratio for those steps that move into new basins. If a negative number is supplied for either, the ratios is printed, but the corresponding parameter is not adjusted.*RBSYM*: specifies that internal symmetry operations permuting equivalent sites for rigid-body building blocks exist. The operations are read in from a file`rbsymops`, which must exist in the working directory. The first line of the file is an integer that specifies the number of operations generated by proper axes of rotation including the identity operation; the operations are then read in one at a time in a representation consisting of a unit vector, defining the axis in the reference frame, and an angle in degrees, describing the magnitude of rotation about that axis. The first operation has to correspond to the identity operation.This keyword has to be combined with

*PERMDIST*so that structures are aligned and a distance metric considered based on permutations of identical rigid bodies and any internal symmetry operation of each rigid body that is a symmetry of the potential energy function.*RELAXFINALQUENCH*: This means final quench is done in atom coordinates. Useful if you want to compare final energies. This is to be used with*RIGIDINIT*keyword.*RESERVOIR n*: for use in combination with*PTMC*. A reservoir of local minima is used for the lowest temperature replicas up to cpu number*n*. The default is , which means that only the lowest replica used the reservoir. Visit statistics are dumped for replicas that use the reservoir, but exchanges only occur when the lowest non-reservoir replica inherits a configuration. This keyword requires files`min.data`and`points.min`in the current working directory in`PATHSAMPLE`format. See also*EXEQ*.*RESIZE resize*: all the coordinates are multiplied by*resize*after they have been read in, before any other operations are performed. This command is useful for scaling results obtained with one potential for a system with a different pair equilibrium distance.*RESTART nrelax nhs*: reseed runs if a step in not accepted within twice*nrelax*steps.*nhs*is the number of hard sphere moves used to produce the new starting configuration. If*nhs=0*(the default) then the geometry is changed by reseeding.*RESTORE dumpfile intEdumpfile*: restore a previous`GMIN`run from a*dumpfile*. The number of basin-hopping steps performed will be the difference between the number requested for the run that produced the dumpfile, minus the number that were completed at the point the dumpfile was created. This option is not available before version 2.3. If you are using the*A9INTE*keyword, you can specify the interaction enthalpy dump file to restore from as a second arguement.*RGCL2*: specifies a DIM rare gas-Cl potential.*RIGIDINIT*: This will turn on the local rigid body framework. This keyword needs two additional input files:*coordsinirigid*and*rbodyconfig*.*coordsinirigid*should contain the coordinates of all the atoms whether they are part of local rigid bodies or not. During initialization, GMIN will select appropriate coordinates and throw away irrelevant ones. The format is:*x1 y1 z1**x2 y2 z2**...**...**xn yn zn*

The file

*rbodyconfig*defines the rigid bodies, with the following format:*GROUP NoAtomsInGroup**Atom 1**Atom 2**...**...**Atom N*

The keywords*RELAXFINALQUENCH*and*NRELAXRIGID*can be used in conjuction with*RIGIDINIT*.*RINGROTSCALE factor*: when applying cartesian moves with CHARMM, amino acid rings are moved as rigid units. Setting*factor*(default 0.0) between 0.0 and 1.0 will apply a random rotation to these rings during step taking. The suggested value is 0.1 to prevent the regular formation of high energy structures.*RKMIN*: specifies a Runga-Kutta minimisation scheme. Very inefficient.*RMS rmslimit rmstol rmssave lca best*: used with*CHARMM*keyword to specify that the RMSD compared to a reference geometry is calculated. The reference geometry must be given in xyz-format in an additional file`compare`.*rmssave*is an integer that specifies the number of lowest energy geometries and RMSD*rmslimit*to save. Geometries are only saved if their RMSD's are more than*rmstol*different. The flag*lca*controls whether the all-atom RMSD (*lca*=0) or the -RMSD (*lca*=1) is calculated. The flag*best*determines which structure is compared to the reference after each quench.*best*=0 implies the current quench minimum and*best*=1 implies the current best (lowest energy) minimum. If*TRACKDATA*is also specified, the RMSD calculated after each quench is produced in the file `rmsd' in gnuplot readable format.*ROTAMER maxchange pselect occuw (centre cutoff)*: Used with AMBER9 only. Specifies that rotamer moves should be taken. Every step, up to*maxchange*rotamers may be selected with a probability*pselect*.*occuw*determines the minimum % occupation a rotamer must have to be selected from the library[29] when making a change. For example,*occuw*restricts possible rotamer choice to those with a greater than 0.4% occupation. If you want to focus rotamer changes around a ligand/binding pocket, the optional*centre*and*cutoff*arguements may be used.*centre*specifies the residue of interest (for example a ligand), and*cutoff*the limiting distance from this centre that rotamers may be changed. The selection probability decreases linearlly from the*centre*residue. To use these moves, you need three files found in the SCRIPTS directory: PdbRotamerSearch, penultimate.lib and rotamermove.csh in your working directory for each run.*ROTAMERMOVE frequency maxrotmoves selectionscheme*: Specifies that rotamer moves should be taken using the sequence-dependent rotamer library. Rotamer moves are made every*frequency*steps and a random number of side chains up to*maxrotmoves*are changed.*selectionscheme*specifies how the amino acids are selected for rotamer moves, currently ``UNIFORM'' is the only option. Rotamers are chosen for a particular amino acid based on its adjacent amino acids and its predicted occupation probability.*ROTATEHINGE freq factor*: For use with the plate-folding potential (but could possibly be used elsewhere as well). An input file`hingeconfig`is used to define hinges between sets of rigid bodies. Every*freq*steps, the set of rigid bodies on the ``moving side'' of the hinge are rotated about the hinge axis by a random angle between and .For each hinge,

`hingeconfig`contains the following three lines:

*nmove*, the number of plates on the ``moving side'' of the hinge*[plate_indices]*, a list of rigid body indices for the moving plates*atom1 atom2 atom3 atom4*.

The hinge axis connects the midpoints of the lines connecting the two pairs (

*atom1*,*atom2*) and (*atom3*,*atom4*). For the plate potential, each of these atom pairs should straddle the hinge and be connected by a stiff spring.*atom1*lies on the same plate as*atom3*.*atom2*and*atom4*are on the opposite side of the hinge.*ROTATERIGID freq factor*: for use with the generalised rigid body framework,*RIGIDINIT*. Randomly rotates each rigid body in the system by a factor of multiplied by*factor*every*freq*steps.*SANDBOX:*Specifies that the sandbox potential should be used. This keyword requires an auxiliary input file`rbdata`and produces an auxiliary output visualization file`sandout.xyz`. See the Sandbox section of this documentation for information on producing rbdata files and for examples.*SAVE nsave*:*nsave*is an integer that specifies the number of lowest energy geometries to save and summarise in the file`lowest`. Arrays are now dynamically allocated, so any positive integer can be specified. Note that if*nsave*is large, minima that are not in the Markov chain might also be written out which might be high energy non-physical conformations.*SAVEFRQS*: save all normal mode frequencies for use with*CNBH*and*FEBH*if a quantum vibrational partition function is required. Creates direct access file`min.frqs`.*SAVEMULTIMINONLY*: specifies that only multiminima are to be considered for the final dump to`lowest`.*SAVEINTE nsaveinte*:*nsaveinte*is an integer that specifies the number of lowest interaction enthalpy geometries to save and summarise in the file`intelowest`. See*A9INTE*.*SEMIGRAND_MU mu_1 ...mu_M*: specifies the semi-grand chemical potentials, relative to the first species, for use in conjunction with the keyword*LFLIPS*. The number of values ought to match the number of different species minus one (i.e.*M=NSPECIES-1*).*SETCENTRE x y z*: Sets the centre of mass/coordinates (before the initial quench) to (*x,y,z*). For example,*SETCENTRE 0.0 0.0 0.0*would translate the centre of mass to the origin.*SETCHIRAL*: For use with*AMBER9*,*NAB*and*AMBER12*keywords. Specifies that the expected chirality of each centre should be maintained based on that in the initial quenched minimum, rather than the standard chiralities found in most proteins/nucleotides. WARNING: Presently for*AMBER12*, without this keyword being included, no chirality checking is done at all!*SC nn mm sig sceps scc*: specifies a Sutton-Chen potential[30] with parameters*nn*,*mm*, =*sig*,*sceps*and*scc*.*SEED nsstop*: if the*SEED*keyword appears then the program looks for a file`seed`containing coordinates, which are used to `seed' the new run. The number of coordinates given in this file should be no more than one less than the number given in`coords`. The specified coordinates are frozen from the first step until step*nsstop*.*SHIFTCUT*: specifies a shifted-truncated potential for bulk binary Lennard-Jones.*SLOPPYCONV bgmax*: specifies a basin-hopping run (as opposed to standard MC on the untransformed surface).*bgmax*is the convergence criterion for the RMS force in the basin-hopping quenches. If this criterion is too strict then the run time will be greatly increased. If it is too sloppy then the performance of the algorithm is impaired. Different values are needed for different potentials.*BASIN*can be used instead.*SORT*: for pairwise potentials the atoms can be sorted from most to least strongly bound. The*SORT*keyword enables this sorting for the coordinates printed in file`lowest`. This can be useful for seeding subsequent runs by removing the most weakly bound atoms. This sort is not set by default and is meaningless if the pair energies are not computed.*SPECLABELS L1 L2 ...LM*: specifies the labels to be used in file`lowest`for each atomic species. Intended for use with a potential invoked by keywords*MLJ*,*MGUPTA*and*MSC*. Note that each label is interpreted as a string of two characters, and the calculation will stop if the supplied number of labels (*M*) does not match the species count.*SPECMASS m1 m2 ...mM*: specifies the mass for each atomic species (all masses are 1 by default). Intended for calculation of a mass-weighted Hessian or molecular dynamics simulations. Error will occur if the supplied number (*M*) of masses does not match the species count.*STAR*: specifies an excited state calculation for Ar or Ne for a diatomics-in-molecules potential when used with*NEON*or*ARGON*.*STEP step astep ostep block*: specifies the maximum step sizes.*step*is for the maximum change of any Cartesian coordinate and*astep*specifies a tolerance on the binding energy of individual atoms (if available, i.e. for Morse and LJ) below which an angular step is taken for that atom. See the following section for more details.*ostep*is the maximum displacement of an axis-angle coordinate for a rigid body system and*block*(an integer) is the block size for which separate translational and orientational displacements will be made for rigid bodies. Omitting*block*or using a value of zero results in translational and orientational steps being taken simultaneously for rigid bodies. The default values for*step*,*astep*and*ostep*are all 0.3 and the default value of*nblock*is zero.*STEEREDMIN smink sminkinc smindiststart smindistfinish sminatoma sminatomb*: specified steered minimisation should be performed (must be used with*AMBER9*). For a protein/ligand system, this adds a translation to the MC move. The vector between the centre of coordinates of groups A and B (as defined in the file movableatoms) is calculated and set to*smindiststart*. During the following minimisation, a restoring force is applied to the ligand. The harmonic force constant is initially zero, and rises by*sminkinc*every LBFGS step up to a maximum of*smink*. The force is applied until the A->B distance is less than*smindistfinish*.*STEPS mcsteps tfac*: determines the length of the basin-hopping run through the integer*mcsteps*and the annealing protocol through the real variable*tfac*. The temperature is multiplied by*tfac*after every step in each run.*STICKY nrbsites, sigma*: specifies a `sticky patch' potential with*nrbsites*sites in the rigid body reference and a value of*sigma*for the parameter.*STOCK mu lambda*: specifies a Stockmeyer potential with parameters and , respectively.*STOCKAA muD E*: calls a finite system of Stockmayer particles, where is the dipole moment strength and the electric field of stength can be optionally present. The field, if present, is along the space-fixed z-direction.*STRAND*: specifies a system of strands coded using the rigid body formalism.*STRESS mode*: calculate and print atomic-level stresses in the file`lowest`. The integer parameter*mode*is optional, with the default value being 1, when the local pressure and the corresponding anisotropy parameter are printed after each atom's coordinates. Per-atom energy is also printed in the final field. Additional modes can be introduced if other invariants of the local stress tensor are desired.*SUPPRESS*: suppresses the majority of the GMIN output. Think of it as the opposite of*DEBUG*.*SW*: specifies the Stillinger-Weber Si potential.*SYMMETRISE int tol1 tol2 tol3 tol4 tol5 qmax mdiff d*: specifies that the symmetrisation routine should be called every*int*steps. The five*tol*parameters are tolerances for various parts of the routine:*tol1*is used in**ptgrp.f**in defining orbits;*tol2*is the distance tolerance used in**ptgrp.f**to define point group symmetry operations;*tol3*is the maximum relative difference in principal moments of inertia used to diagnose point groups with degenerate irreducible representations in**ptgrp.f**;*tol4*is the distance cutoff used to determine if a symmetry element has been lost in**symmetry.f**. Since we are dealing with approximate symmetries, this parameter may be larger than*tol2*. It is compared to the largest atomic displacement divided by the corresponding radius for the closest permutation.*tol4*is also used to test whether atoms lie on a given symmetry element, and in testing whether orbits generated from `floaters' are actually contained in the core.*tol5*is generally to check for atom clashes in**symmetry.f**, including analysis of missing sites in orbits, as well as overlap between orbits generated from `floaters' and previous core or new orbit sites.*qmax*is the maximum number of quenches allowed for each call to**symmetry.f**.*mdiff*is used to test whether a generated symmetry operation is new. If any of the nine components of the corresponding matrix differs by more than*mdiff*from an existing matrix then the operations are considered to be different.*d*is the exponential factor used in constructing a centre of mass that is biased towards core atoms. The contribution of each atom is weighted by , where is the centre of mass distance of atom on the previous cycle.*TABOO nlist*: specifies a taboo list of the*nlist*lowest minima should be maintained.*TARGET target1 target2*: specifies any number of target energies. The current run stops in an orderly fashion if the current quench energy is within*econv*of any target (see*EDIFF*).*TEMPERATURE temp*: defines the temperature,*temp*, at which the MC runs are conducted. Different values can be specified for serial `parallel' runs if*PARALLEL*is set. For true parallel basin-hopping use the*BHPT*keyword and omit*TEMPERATURE*.*TETHER hdistconstraint hwindows ExtrapolationPercent lnHarmFreq*: requests a calculation of the vibrational density of states for a given minimum.*hdistconstraint*is the minimised average radius of the basin of attraction to which the minimum belongs,*hwindows*is the number of potential energy windows into which a WL simulation is split.*ExtrapolationPercent*is the percentage of the whole potential energy spectrum, for which the density of states is estimated from the harmonic approximation and not sampled.*lnHarmFreq*the log product of positive Hessian eigenvalues.*THOMSON q*: specify the Thomson problem for unit charges on a sphere. If*q*is present it is taken to be the charge on one particle, which can therefore be different from all the other unit charges and is read as a real number.*TIGHTCONV cgmax*: cgmax is the tolerance for the RMS force in the final set of quenches that are used to produce the output for file`lowest`. The default is*cgmax*, but the appropriate values depend upon the system in question.*QMAX*can be used instead.*TIP n*: specifies a TIP*n*P intermolecular potential for rigid body water molecules. .*TIP4PGR*: specifies genrigid implementation of TIP4PGR intermolecular potential for rigid body water molecules. Requires files`coordsinirigid`and`rbodyconfig`.*TOLBRENT tolb*: parameter for*DBRENT*minimisation. Inefficient compared to LBFGS.*TOMEGA*: used with the*CHARMM*keyword to specify that peptide bonds will be twisted along with all other dihedrals.*TOSI app amm apm rho*: specifies the Tosi-Fumi potential[31] with parameters , , and .*TRACKDATA*: produces `energy.dat' and `markov.dat' containing the quench number and associated energy and markov energy in two columns and `best.dat', containing the current quench number and the current lowest total energy. If*RMS*is also specified, a file called `rmsd.dat' is produced containing the RMSD from a reference structure. See*RMS*for more information. This allows plotting with gnuplot to monitor convergence of multiple runs. If*A9INTE*is also specified, two additional output files are produced, `intE.dat' containing the quench number and associated interaction enthalpy, and `bestintE.dat' containing the quench number and current lowest interaction enthalpy. This keyword does not yet function for MPI runs.*TRANSLATERIGID freq maxdist*: for use with the generalised rigid body framework,*RIGIDINIT*. Randomly translates each rigid body in the system by a distance up to*maxdist*every*freq*steps.*TSALLIS q*: specifies that steps are accepted/rejected using Tsallis statistics with the given value of*q*, rather than the usual Boltzmann condition.*TTM3*: specifies Xantheas' TTM3-F water potential, coded by Jeremy Richardson. The atom order must be O1, O2,..., H1a, H1b, H2a, H2b,.... The energy is in kcal/mol and the distance unit is Å. Hydrogens are NOT permutable between different oxygens. Note that this potential is prone to cold fusion--setting the*COLDFUSION*parameter explicitly may be necessary.*TWOPLUS*: when combined with keywords*NEON*or*ARGON*uses a diatomics-in-molecules potential for the doubly charged cation.*UACHIRAL*: MUST be included when using ff03ua, the AMBER united atom forcefield unless you have disabled the checks for inverted chiral carbons with*NOCHIRALCHECKS*.*UACHIRAL*ensures the correct impropers are used to define sidechain chirality when HB hydrogen is missing.*UNIFORMMOVE*: the proposed steps for each atom in**takestep**are uniformly distributed over a sphere whose radius is adjusted on-the-fly to give the required acceptance ratio (or fixed if*FIXSTEP*or*FIXBOTH*is set). The default behaviour for backwards compatibility is for the separate , and displacements of each atom to be scaled uniformly within the current step size range.*UPDATES nup*:*UPDATES*is the number of previous steps saved in the LBFGS routine, default 4.*UPDATERIGIDREF*: Updates the rigid body reference coordinates after a step has been taken when using*RIGIDINIT*. This allows steps to be taken within rigid bodies if required. As unphysical conformations may be introduced into the rigid bodies this way,*HYBRIDMIN*should be allowed these to be relaxed.*USEFRQS*: use normal mode frequencies for*CNBH*if a quantum vibrational partition function is required. Accesses file`min.frqs`. Without this keyword the high temperature classical vibrational partition function is used in*CNBH*and*FEBH*.*USEROT*: Include the rigid rotor partition function during a free energy basin-hopping run.*USEMINDATA n*: create a`min.data`file for use with*CNBH*. If*USEFRQS*is set then a*min.frqs*file (direct access) is also created. Unless*NOPOINTS*is set a`points.min`file will also be curated. The`min.data`file has the same format as for`PATHSAMPLE`but there is an extra column specifying the number of atoms.*n*is the maximum number of atoms. This value is needed to set the direct access record size for`min.frqs`and`points.min`files. The maximum size set for*GCBH*needs to be smaller than*n*.*VGW ljsigma ljepsilon taumaxsg taumaxfg*: Specifies use of VGW quantum quenching in place of classical minimization routines such as LBFGS.*ljsigma*and*ljepsilon*are the corresponding Lennard-Jones parameters that must be specified, and taumaxsg and taumaxfg are the maximum value of ``imaginary'' time (inverse tempertaure) for the propagation. The former pertains to the faster ``single-particle'' SP-VGW used for quenching during the MC runs, and the latter for the more accurate ``fully-coupled'' VGW used for the final quenching (analogous to the tight convergence of the LBFGS). A of at least 2.5 is recommended for the SP-VGW and 5.0 for the FC-VGW. A file*vgwdata*containing the masses (in a.m.u.) of all particles, in order of the location of their*xyz*coordinates in ``*coords*'' must be present (e.g. for a 38 atom Ne cluster,*vgwdata*will have 38 lines of ``*20*''). Different masses are permitted, though the current version allows for only one set of LJ parameters.*VGWCPS on magnitude*: Specifies use of contraining potential for SP-VGW (sloppy convergence), as clusters expand during quantum quenching with decreasing mass. 1 or 0 for*on*corresponds to on/off, and magnitude should range from 1 to 1000, with 1 having minimal effect, 1000 being highly constrained. Default value is ``on'', with magnitude 1.*VGWCPF on magnitude*: Same as VGWCPS but for FC-VGW, used for the final, full quenching (tight convergence).*VGWTOL magnitude*: Absolute tolerance parameter for differential equation solver used for VGW quenching. Default value is 0.0001. For highly quantum or ``stiff'' systems this may need to be increased, while it may be decreased for ``softer'' or less quantum systems to enhance speed.*VISITPROP*: if specified the Wang-Landau convergence is governed by proportionality of visits to the current value of the modification factor, and not the histogram flatness criterion [4].*WELCH*: specifies a Welch binary salt potential with the parameters indicated.*ZETT1*and*ZETT2*: specify the Zetterling potentials.

David Wales 2018-07-21