MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories and perform a variety of analyses, including fast RMSD, solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj is the wide variety of molecular dynamics trajectory file formats which are supported, including RCSB pdb, GROMACS xtc and trr, CHARMM / NAMD dcd, AMBER binpos, AMBER NetCDF, AMBER mdcrd, TINKER arc and MDTraj HDF5.

The installation of MDTraj on Helix & Biowulf also contains MDAnalysis, another python package for analyzing MD trajectories.

References:

• McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernández CX, Schwantes CR, Wang LP, Lane TJ, Pande VS. MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophys J. 2015 Oct 20;109(8):1528-32.

• MDTraj Documentation
• MDAnalysis Documentation

• Module Name: mdtraj (see the modules page for more information)
• Singlethreaded
• Environment variables set
  • MDTRAJ_EXAMPLES
• Example files in $MDTRAJ_EXAMPLES

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load mdtraj
[user@cn3144 ~]$ python
>>> import mdtraj as md
>>> t = md.load('trajectory.xtc', top='trajectory.pdb')
>>> print t
<mdtraj.Trajectory with 100 frames, 22 atoms at 0x109f0a3d0>
>>> quit()
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a python input script mdtraj.py. This is an example lifted from the MDTraj Introduction page.

#!/usr/bin/env python
import mdtraj as md
t = md.load('trajectory.xtc', top='trajectory.pdb')
print t
print t[1:10]
print t[-1]
print t.xyz.shape
print np.mean(t.xyz)
print t.time[0:10]
t.unitcell_lengths[-1]
t[::2].save('halftraj.h5')
t[0:10].save_dcd('first-ten-frames.dcd')
atom_to_keep = [a.index for a in t.topology.atoms if a.name == 'CA']
t.restrict_atoms(atoms_to_keep)  # this acts inplace on the trajectory
t.save('CA-only.h5')

Create a batch script mdtraj.sh:

#!/bin/bash
module load mdtraj
python mdtraj.py

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] mdtraj.sh

Create a swarmfile (e.g. mdtraj.swarm). For example:

python mdtraj_1.py
python mdtraj_2.py
python mdtraj_3.py
python mdtraj_4.py

Submit this job using the swarm command.

swarm -f mdtraj.swarm [-g #] [-t #] --module mdtraj