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Information

Purpose: Molecular Dynamics
Latest version: 1.0 beta
License: GNU GPL
Website:  https://westpa.github.io/westpa/sphinx_index.html extlink-icon

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.err
#SBATCH -o westpa_example.out
#SBATCH -p std
#SBATCH -N 1
#SBATCH -n 1

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

INPUT_DIR=$PWD
OUTPUT_DIR=$PWD

./init.sh >& init.out
./run.sh >& run.out

 

Sbatch options:

  • -J: Specify a name for the job allocation. The default is the name of the batch script.
  • -e: Specify a name for the error output file.
  • -o: Specify a name for the output file.
  • -p: Specify the name of the partition (queue) where the job will be submited. The default is std.
  • -N: Number of nodes requested for allocation.
  • -n: Number of processes requested for allocation.

 

 

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