MOLDYN:
This software package provides extensive tools for fast, robust and stable clustering of molecular dynamics trajectories. The essential functions are:
- density-based geometric clustering for microstate generation
- dynamic clustering based on the Most-Probable-Path algorithm (MPP)
- variable dynamic coring for boundary corrections
- dynamic noise assignment.
Additionally, the package includes tools to efficiently filter original coordinates or order parameters based on a discrete state definition to identify representative structures and variables of clusters.
Following is the sample SLURM script that you can take reference:
#!/bin/bash
#SBATCH --job-name=traj_wat
##SBATCH -A chemistry
#SBATCH --nodes=5
#SBATCH --ntasks-per-node=8
#SBATCH --time=14-00:00:00
#SBATCH --error=err.job.%J
#SBATCH --output=out.job.%J
module load apps/precompiled/gaussian/16
export NX=/home/stud/h.baliyan/NEWTON-X/NX-2.2-B09/bin
$NX/moldyn.pl > moldyn.log