PATHSAMPLE website

PATHSAMPLE: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis

PATHSAMPLE is distributed free of charge under the GPL as part of the current svn software image from the group.

Example input

The example input provided here has been tested with the version of PATHSAMPLE specified in the README file within each archive. If it no longer works with a more recent version, please inform a member of the Wales group.

Example for translating a rate matrix into free energy data using GMIN for anaysis by PATHSAMPLE. Download tar file of the directories.
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 input and output for a PATHSAMPLE run using the SBATCH keyword to put OPTIM jobs on the slurm queue, rather than FORK and WAIT. The system is LJ₃₈ and this is s SHORTCUT BARRIER run.
Example input and output for the water₂₁ cluster using the OPTIM interface to xtb and the GFN2 level of theory. Includes a disconnectivity graph setup.
Example input and output for the water₂₁ cluster using the OPTIM interface to xtb and the GFNFF level of theory. Includes a disconnectivity graph setup.
Example input and output for an RNA landscape using AMBER12.
Example input and output for INITIALDISTANCE keyword with DIJINITSTART.
Example pathdata file for CONNECTPAIRS keyword.
Example for LJ13 using NEWCONNECTIONS keyword to grow a database using single-ended transition state searches.
TIP4P water octamer using angle-axis coordinates
A PATHSAMPLE database for the LJ₃₈ cluster containing 100000 minima.
A PATHSAMPLE run for the LJ₃₁ cluster using the ADDMINXYZ keyword to read in minima from an xyz file and create min.data and points.min.
PATHSAMPLE and OPTIM input to create initial connections between two binding modes for the Influenza HA protein of four H1N1 strains. Also includes an example refined database used in a pulication currently in review (February 2015).
PATHSAMPLE databases for the trpzip potential energy landscape at different levels of local rigidification.
Generating a PATHSAMPLE database for Tryptophan Zipper 1 using AMBER12 and the NapShift hybrid potential.
PATHSAMPLE database for the Chignolin potential energy landscape computed using AMBER.
Example submission script for running PATHSAMPLE jobs with the SLURM queueing system
Example input for use of CHECKSPMUTATE with CHECKMIN. On CUDA with AMBER12. Changing from wt HemS+haem+NADH system to wt ChuS+haem+NADH system.

[Source] [Documentation]