VOTCA

Overview

VOTCA is a software package which focuses on the analysis of molecular dynamics data, the development of systematic coarse-graining techniques as well as methods used for simulating microscopic charge transport in disordered semiconductors.
The following versions are installed on the CSF:

• Votca 1.2.3 – includes gromacs 4.6.0 (multi-threaded single precision only) in the VOTCA directory.

VOTCA has not been tested using any of the existing gromacs installs.

Restrictions on use

All users may use the software. All users should cite their use of the software as per the VOTCA Citations webpage.

Set up procedure

To access the executables please load one of the appropriate modulefile:

module load apps/intel-12.0/votca/1.2.3

Running the application

Please do not run VOTCA on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

VOTCA is not suitable for serial jobs. Some components default to using all the cores available on a compute node and can therefore cause issues to other running jobs.

Parallel batch job submission

• It is recommended that you request a whole node for your job. There are a number of node types to choose from – please see the examples below.
• smp.pe is the only suitable parallel environment, VOTCA cannot run on more than one node.

Westmere Intel nodes

#! /bin/bash -e
#$ -cwd
#$ -V
#$ -l westmere
#$ -pe smp.pe 12

grompp -v 

mdrun -v -nt $NSLOTS

echo Calculating distributions
csg_stat --top topol.tpr --trj traj.trr --cg hexane.xml --nt $NSLOTS --options fmatch.xml

echo "Mapping confout.gro to get configuration for coarse-grained run"
csg_map --top topol.tpr --trj confout.gro --cg hexane.xml --out conf_cg.gro

Further info

• Documentation: VOTCA Website
• Manpages, e.g. man csg_stat
• Tutorials/examples are available in $VOTCA_HOME/csg-tutorials

Updates

None.