GromacsOnEUREKA (GROMAX)

GromacsOnEUREKA is a repository of useful scripts and documentation for using GROMACS for molecular dynamics simulations on the University of Surrey's "EUREKA" HPC cluster.

This page includes installation information, and descriptions/usage of functions included. A step-by-step guide for MD in Gromacs on EUREKA can be found in the wiki.

• Installation
• Usage
  • Load Gromacs
  • Interface with Gromacs
  • Prepare PDBs for Gromacs
  • Analysis using AMP
  • Example with 3PJR

Installation

Install the requirements for the use-cases you deem necessary.

Requirements for general use

• Clone and set up MShTools

Requirements for use within ASE

• Install ASE
• Clone and set up MPyTools
• Clone and set up AseMolPlot

Installation

• Clone this repository cd; git clone https://gitlab.eps.surrey.ac.uk/mw00368/GromacsOnEUREKA
• Add the following to your ~/.bash_profile:
  • export GROMAX="/path/to/GromacsOnEUREKA"
  • export PATH=$PATH:$GROMAX

Usage

Load Gromacs

Source load_gmx.sh to load and set up Gromacs:

source load_gmx.sh

This is for both interactive sessions and scripts.

Interface with Gromacs

Functions to make Gromacs on EUREKA simpler can be found in gmx_funcs.sh. Source to use the functions:

source gmx_funcs.sh

The "gromax" wrapper for Gromacs

Included in gmx_funcs.sh is a function called gromax which adds additional input arguments, logging (console redirection), verbosity, and error catching to the Gromacs executable.

For example calling:

gromax grompp -l 5 -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr

will write to the console:

Running grompp 5...

then will call Gromacs for you and upon completion:

Running grompp 5... Done, exit code: 0 Fri 20 Mar 17:50:43 GMT 2020.

With the full Gromacs output and error log being written to _grompp5.log. If the exit code is non-zero the script will be stopped to prevent further errors and wasting HPC resources on processes that are doomed from the start.

Plotting xvg's produced by "gromax energy"

gmx_funcs.sh contains the function xvg2png which calls the GNUPlot script xvg2png.gp. For usage run xvg2png --help.

Wrapper for "amp_stats.py"

A wrapper function with logging functionality exists as:

dnaBondStats -l $LOGNUM

Prepare PDBs for Gromacs

pdb_mod.sh

Tools to modify PDB's for use within Gromacs.

Available methods:

• Summary of a PDB
• Find a residue entry in a given force field
• List all instances of an atom name in a PDB
• Replace all entries with a given atom name with another in a PDB
• Remove a chain from a PDB

For detailed usage information run pdb_mod.sh --help and see the wiki.

Analysis using AMP

The python script ase_stats.py uses AseMolPlot to perform analysis and produce graphs.

Currently it supports:

• Converting a trajectory (.pdb from gmx trjconv) to an ASE Trajectory (.traj)
• Plotting lengths of hydrogen bond interactions between matching DNA base pairs.

For minimal instructions run:

amp_stats.py -h

Example with 3PJR

run_3pjr.sh

Example MD script.