GROMACS v4.6.1

Overview

GROMACS is a package for computing molecular dynamics, simulating Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is designed for biochemical molecules with complicated bonded interactions (e.g. proteins, lipids, nucleic acids) but can also be used for non-biological systems (e.g. polymers).

Please do not add the -v flag to your mdrun command. It will write to a log file every second for the duration of your job and can lead to severe overloading of the file servers.

This version is v4.6.1 (with and without the Plumed 1.3 plugin). PLUMED is an open source plugin for free energy calculations in molecular systems. The following flavours are available:

• Single and double precision multi-threaded (OpenMP) versions: mdrun and mdrun_d
• Single and double precision MPI (not threaded) versions: mdrun_mpi and mdrun_d_mpi
• Single and double precision MPI (not threaded) with Plumed 1.3 plugin patch applied to source code: mdrun_mpi and mdrun_d_mpi
• Compiled with Intel 12.0.5 compiler, Intel MKL 10.3u5 providing the FFT functions.

Bugfix for g_hbond

Version 4.6.1 has the g_hbond fix included by default and so no separate build has been made for this version. See the GROMACS v4.5.4 CSF documentation for a description of that issue.

Restrictions on use

GROMACS is free software, available under the GNU General Public License.

Set up procedure

You must load the appropriate modulefile:

module load modulefile

replacing modulefile with one of the modules listed in the table below.

For the version of GROMACS installed with the unmodified source code extracted from gromacs-4.6.1.tar.gz use:

Version	Modulefile	Notes
Single precision multi-threaded	apps/intel-12.0/gromacs/4.6.1/single	non-MPI
Double precision multi-threaded	apps/intel-12.0/gromacs/4.6.1/double	non-MPI
Single precision MPI	apps/intel-12.0/gromacs/4.6.1/single-mpi	For MPI on Intel nodes using gigabit ethernet
Single precision MPI – Infiniband	apps/intel-12.0/gromacs/4.6.1/single-mpi-ib	For MPI on Intel or AMD nodes using infiniband
Double precision MPI	apps/intel-12.0/gromacs/4.6.1/double-mpi	For MPI on Intel nodes using gigabit ethernet
Double precision MPI – Infiniband	apps/intel-12.0/gromacs/4.6.1/double-mpi-ib	For MPI on Intel or AMD nodes using Infiniband

For the version of GROMACS installed with the Plumed 1.3 patched source code extracted from gromacs-4.6.1.tar.gz use:

Version	Modulefile	Notes
Single precision MPI	apps/intel-12.0/gromacs/4.6.1_plumed/single-mpi	For MPI on Intel nodes using gigabit ethernet
Single precision MPI – Infiniband	apps/intel-12.0/gromacs/4.6.1_plumed/single-mpi-ib	For MPI on Intel or AMD nodes using infiniband
Double precision MPI	apps/intel-12.0/gromacs/4.6.1_plumed/double-mpi	For MPI on Intel nodes using gigabit ethernet
Double precision MPI – Infiniband	apps/intel-12.0/gromacs/4.6.1_plumed/double-mpi-ib	For MPI on Intel or AMD nodes using Infiniband

Plumed 1.3 Notes

1. Plumed does not work with multi-threaded Gromacs. Hence only MPI versions are available. If you require single-threaded non-MPI versions of Gromacs for use with Plumed please contact its-ri-team@manchester.ac.uk.
2. The Plumed utilities are available in your PATH once one of the above plumed modulefiles has been loaded. These include:
   • bias-exchange.sh
   • driver
   • exchange-tool.x
   • plumed_standalone
   • reweight
   • sum_hills.x
   • sum_hills_mpi.x
3. For the Plumed manual run: evince $PLUMEDHOME/manual/manual.pdf

Running the application

First load the required module (see above) and create a directory containing the required input data files.

You MUST ensure that as well as requesting a number of cores from a suitable parallel environment you also tell gromacs how many cores it may use. These two numbers must be the same, which can be ensured through correct use of some variables and/or flags depending on the version of gromacs being used. Failure to set this information causes gromacs to run incorrectly, overload compute nodes and potentially trample on jobs belonging to other users. All of the examples below ensure that jobs use the cores requested.

Please do not add the -v flag to your mdrun command. It will write to a log file every second for the duration of your job and can lead to severe overloading of the file servers.

Multi-threaded single-precision, 2 to 24 cores

Note that GROMACS v4.6.1 (unlike v4.5.4) does not support the -nt flag to set the number of threads when using the multithreaded OpenMP (non-MPI) verison. Instead set the OMP_NUM_THREADS environment variable as shown below.

An example batch submission script to run the single-precision mdrun executable with 12 threads:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 12

export OMP_NUM_THREADS=$NSLOTS
mdrun

Submit with the command: qsub scriptname

Note: smp.pe is the only pe suitable for multi-threaded GROMACS. 16 cores the maximum job size in that PE.

Multi-threaded double-precision, 2 to 24 cores

An example batch submission script to run the double-precision mdrun_d executable with 12 threads:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 12

export OMP_NUM_THREADS=$NSLOTS
mdrun_d

Submit with the command: qsub scriptname

Note: smp.pe is the only pe suitable for multi-threaded GROMACS. 24 cores is the maximum job size in that PE.

Single-precision MPI with Infiniband, 48 cores or more in multiples of 24

An example batch submission script to run the single precision mdrun_mpi executable with 48 MPI processes on 48 cores with the orte-24-ib.pe parallel environment (Intel nodes using InfiniBand):

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe orte-24-ib.pe 48

mpiexec -n $NSLOTS mdrun_mpi

Submit with the command: qsub scriptname

Notes

• orte-24-ib.pe – you must request multiples of 24 and a minimum of 48.
• If you wish to use the AMD nodes please use orte-32-ib.pe – you must request multiples of 32.

Double precision MPI with Infiniband, 48 or more in multiples of 24

An example batch submission script to run the double precision mdrun_d_mpi executable with 48 MPI processes on 48 cores with the orte-24-ib.pe parallel environment (Intel nodes using infiniband):

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe orte-24-ib.pe 48

mpiexec -n $NSLOTS mdrun_d_mpi

Submit with the command: qsub scriptname

Notes

• orte-24-ib.pe – you must request multiples of 24 and a minimum of 48.
• If you wish to use the AMD nodes please use orte-32-ib.pe – you must request multiples of 32.

I want to use a number of cores not recommended above, what are the options?

Please contact its-ri-team@manchester.ac.uk for advice.

Further info

• You can see a list of all the installed GROMACS utilities with the command: ls $GMXDIR/bin
• GROMACS web page
• GROMACS manuals
• GROMACS user mailing list

Updates

Nov 2013 – Documentation for 4.5.4 and 4.6.1 split in to two pages.
May 2013 – Gromacs 4.6.1 and Plumed 1.3 installed.