Example input and output

• Basic example for LJ38
• Bsain-hopping parallel tempering (BHPT using MPI) example for LJ38 - tar.bz2 file
• Examples for Stillinger-Weber potential with periodic boundary conditions. The 64fixed directory corresponds to 64 atoms in a fixed cell. The 64variable directory contains subdirectories for variable cell optimisations at pressures of 0 GPa and 12 GPa.
• Force field parameters for ReaxFF from Development of ReaxFF Reactive Force Field for Aqueous Iron-Sulfur Clusters with Applications to Stability and Reactivity in Water. Journal of chemical information and modeling (2021) 61, 1204
• A detailed tutorial for exploring the energy landscape of peptides using GMIN/OPTIM/PATHSAMPLE programs interfaced with AMBER.
  Steps to obtain and further analyse the heat capacity as a function of temperature are also explained, as well as basin-hopping parallel tempering. The entire procedure is explained in steps starting from the sequence only.
• example for translating a rate matrix into free energy data for anaysis by PATHSAMPLE. Download tar file of the directories.
• Hexapeptide grouprotation example for AMBER20. Can be run with BHPT for MPI enabled GMIN.
• Hexapeptide dimer example for AMBER20, including a rigid body monomer moves. Can be run with BHPT for MPI enabled GMIN.
• crystal structure prediction for benzene. See J Phys Chem A (2021) 125, 3776 (DOI: 10.1021/acs.jpca.1c00903)
• QUIP GAP potential for Si₇
• QUIP GAP potential for C₇
• QUIP GAP potential for C₆₀
• CASTEP with xtb guiding potential nest example for pentaprismane
• Tapered ReaxFF input and output for Au20
• DFTB+ input and output for C60
• xtb input and output for water₂₁
• TIP4P water octamer
• TIP4P water octamer permutational distance optimisation
• Tryptophan Zipper 1 examples (pdb 1LE0) for CHARMM with FACTS implicit solvent model. The move types include STANDARD, LOOPMODEL, CART, and NEIGHBOURS, with corresponding data and output files. Note that auxiliary files are needed for some of these keywords.
• Tryptophan Zipper 1 with NapShift hybrid potential (pdb 1LE0) example input and output for PDB 1LE0 using the NapShift hybrid potential with AMBER12.
• VGW quantum quenching minimisation for 125 atom cluster
• Local rigid body example with AMBER force field - chignolin
• Local rigid body example with CHARMM force field - trpzip
• Factorised superposition approach (FSA) for computing binding free energies
• CamShift example with CHARMM force field - trpzip
• Basin-hopping for adatoms on a Sutton-Chen metal surface (001) - tar.bz2
• Basin-hopping with biminimisation for Cu8Ag4Au7 nanoalloy modelled using the Gupta potential - tar.bz2
• Generalised basin-hopping in the space of bi- and triminima for Gupta nanoalloys - tar.bz2
• Single quench using CUDA and AMBER 12 for aldose reductase.
• REAXFFGMIN on Glycine with GROUPROTATION moves.

  Example input for basin-hopping and genetic algorithm runs for the P46 and P69 model proteins corresponding to the results described in M.T. Oakley, R.L. Johnston and D.J. Wales, J. Phys. Chem. B, 115, 11525-11529 (2011):

• A simple 10-generation GA optimisation of P46 with none of the extra optimisation keywords.
• Optimal settings for all of the GA keywords.
• Basin-hopping for P69.
• Basin-hopping for a P46 Go model.