Purpose: Molecular Dynamics
Latest version: 1.0 beta
License: (tick) Free of use
                 GNU GPL _ext-link
Website: https://westpa.github.io/ _ext-link

The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis (WESTPA) is a high-performance framework for carrying out extended-timescale simulations of rare events with rigorous kinetics using the weighted ensemble algorithm of Huber and Kim (1996).

The software works with any dynamics engine and has already been used with a variety of molecular dynamics (e.g. GROMACS, NAMD, AMBER) and cell-modeling packages (e.g. BioNetGen, MCell).

SLURM Submit script example

For more information use the Job Script Generator.


starccm_example.slm
#!/bin/bash
#SBATCH -J westpa_example
#SBATCH -e westpa_example.%j.err
#SBATCH -o westpa_example.%j.out
#SBATCH -p std
#SBATCH -n 1
#SBATCH -t 0-02:00

module load apps/westpa/2017.10
module load apps/gromacs/2018.1

##
#  Modify the input and output files!
cp -r ${SLURM_SUBMIT_DIR}/{init.sh,run.sh} ${SCRATCH}
cd ${SCRATCH}
 
srun init.sh >& init.out
srun run.sh >& run.out
 
cp ./{init.out,run.out} ${SLURM_SUBMIT_DIR}

Sbatch options:

The options shown in the example are detailed below. For more information and a more comprehensive list of available options, see the sbatch command page.

  • -J: Name for the job's allocation.
  • -e: Name of the stderr redirection filename.
  • -o: Name of the stdout redirection filename.
  • -p: Name of the partition (queue) where the job will be submitted.

  • -n: Number of tasks.

  • -c: Number of cores per task.
  • -t: Set the job's time limit. If the job don't finish before the time runs out, it will be killed.



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