GROMACS v5.1.4

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).

Significant Change in this Version

As of Gromacs v5.1.x, the different gromacs commands (e.g., mdrun, grompp, g_hbond) should now be run using the command:

gmx command

where command is the name of the command you wish to run (without any g_ prefix), for example:

gmx mdrun

The gmx command changes its name to reflect the gromacs flavour being used but the command does not change. For example, if using the mdrun command:

# New 5.1.4 method                     # Previous 5.0.4 method
gmx   mdrun                            mdrun
gmx_d mdrun                            mdrun_d
mpirun -n $NSLOTS gmx_mpi   mdrun      mpirun -n $NSLOTS mdrun_mpi
mpirun -n $NSLOTS gmx_mpi_d mdrun      mpirun -n $NSLOTS mdrun_mpi_d

The complete list of command names can be found by running the following on the login node:

module load apps/intel-14.0/gromacs/5.1.4/single
gmx help commands

# The following commands are available:
anadock			dyecoupl		mdmat		sans
anaeig			dyndom			mdrun		sasa
analyze			editconf		mindist		saxs
angle			eneconv			mk_angndx	select
bar			enemat			morph		sham
bundle			energy			msd		sigeps
check			filter			nmeig		solvate
chi			freevolume		nmens		sorient
cluster			gangle			nmtraj		spatial
clustsize		genconf			order		spol
confrms			genion			pairdist	tcaf
convert-tpr		genrestr		pdb2gmx		traj
covar			grompp			pme_error	trjcat
current			gyrate			polystat	trjconv
density			h2order			potential	trjorder
densmap			hbond			principal	tune_pme
densorder		helix			rama		vanhove
dielectric		helixorient		rdf		velacc
dipoles			help			rms		view
disre			hydorder		rmsdist		wham
distance		insert-molecules	rmsf		wheel
do_dssp			lie			rotacf		x2top
dos			make_edi		rotmat		xpm2ps
dump			make_ndx		saltbr

Notice that the command names do NOT start with g_ and do NOT reference the flavour being run (e.g., _mpi_d). Only the main gmx command changes its name to reflect the flavour (see below for list of modulefiles for the full list of flavours available).

To obtain more help about a particular command run:

gmx help command

For example

gmx help mdrun

Helper scripts

To assist with moving to the new command calling method, we have recreated some of the individual commands that you may have used in your jobscript. For example, you can continue to use mdrun (or mdrun_d) instead of the new gmx mdrun (or gmx_d mdrun) in this release. These extra commands are automatically included in your environment when you load the gromacs modulefiles. This old method uses the flavour of gromacs in the command name (see above for comparison of new and old commands).

However, please note that the following commands are new to v5.1.4 and so can only be run using the new method (gmx command):

# New commands that can only be run using: gmx command

check			help
convert-tpr		insert-molecules
distance		pairdist
dump			sasa
freevolume		solvate
gangle			view

Available Flavours

This version is v5.1.4. The following flavours are available:

5.1.4 for all Intel node types

Note: ability to run on all Intel nodes implies lower optimization.

• 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
• Compiled with Intel 14.0.3 compiler with the associated Intel MKL providing the FFT functions.
• ngmx has been included.

5.1.4 for Sandybridge and Ivybridge (and Haswell, Broadwell nodes) only

Note: ability to run on only Sandybridge, Ivybridge (and Haswell) nodes implies higher optimization. Note that an even higher level of optimization, and an MPI version, is available for Haswell nodes (see below).

• Single and double precision multi-threaded (OpenMP) versions: mdrun and mdrun_d
• Compiled with Intel 14.0.3 compiler with the associated Intel MKL providing the FFT functions and with AVX_256 (an instruction set specific to these nodes) so WILL NOT work on Westmere nodes and NONE of the commands can be run on the login nodes.
• We have no Sandybridge or Ivybridge nodes connected by Infiniband which means ONLY smp.pe (single-node, multicore) jobs for these types nodes.
• There are no MPI versions of 5.1.4 for Sandybridge and Ivybridge nodes available on the CSF.
• This version will not run on highmem, twoday or short nodes (they are all Westmere).
• ngmx has been included.

5.1.4 for Haswell and Broadwell nodes only

Note: ability to run on only Haswell and Broadwell nodes implies higher optimization.

• Single and double precision single-node, multi-threaded (OpenMP) versions: mdrun and mdrun_d
• Single and double precision multi-node (MPI) versions: mdrun_mpi and mdrun_mpi_d
• Compiled with Intel 14.0.3 compiler with the associated Intel MKL providing the FFT functions and with AVX2_256 (an instruction set specific to these nodes which provides further optimization than AVX_256) so WILL NOT work on Westmere, Sandybridge and Ivybridge nodes.
• Single-node multi-core smp.pe jobs can use these nodes.
• Multi-core MPI orte-24-ib.pe jobs can use these nodes – the Haswell and Broadwell nodes have InfiniBand networking.
• This version will not run on highmem, twoday or short nodes (they are all Westmere).
• ngmx has been included.

Bugfix for g_hbond

Version 5.1.4 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.

qrsh -l inter -l short -l sandybridge

Running the application in batch

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

Please NOTE the following which important for running jobs correctly and efficiently:

Ensure you inform gromacs how many cores it can use. This is done using the $NSLOTS variable which is automatically set for you in the jobscript to be the number of cores you request in the jobscript header (see later for complete examples). You can use either of the following methods depending whether you want a multi-core job (running on a single compute node) or a larger job running across multiple compute nodes:

# Multi-core (single-node) or Multi-node MPI jobs

mpirun -n $NSLOTS mdrun_mpi         # Old method (v5.0.4 and earlier)
mpirun -n $NSLOTS mdrun_mpi_d       # Old method (v5.0.4 and earlier)

mpirun -n $NSLOTS gmx_mpi mdrun     # New method (v5.1.4 and later)
mpirun -n $NSLOTS gmx_mpi_d mdrun   # New method (v5.1.4 and later)

or

# Single-node multi-threaded job

export OMP_NUM_THREADS=$NSLOTS      # Do this for all versions
mdrun                               # Old method (v5.0.4 and earlier)
mdrun_d                             # Old method (v5.0.4 and earlier)

export OMP_NUM_THREADS=$NSLOTS      # Do this for all versions
gmx mdrun                           # New method (v5.1.4 and later)
gmx_d mdrun                         # New method (v5.1.4 and later)

The examples below can be used for single precision or double precision gromacs. Simply run mdrun (single precision) or mdrun_d (double precision).

Multi-threaded single-precision on Intel nodes, 2 to 24 cores

Note that GROMACS v5.1.4 (unlike v4.5.4) does not support the -nt flag to set the number of threads when using the multithreaded OpenMP (non-MPI) version. 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            # Can specify 2 to 24 cores in smp.pe
                            # 2-12 includes Westmere, Sandybridge, Ivybridge, Haswell, Broadwell
                            # 13-16 forces use of Ivybridge
                            # 17-24 forces use of Haswell or Broadwell
                            # Can force use of a particular architecture (see below)

export OMP_NUM_THREADS=$NSLOTS
mdrun
  #
  # This is the old naming convention (it will still work in this release)
  # The new gromacs convention is to run: gmx mdrun

Submit with the command: qsub scriptname

The system will run your job on a Westmere, a Sandybridge or an Ivybridge node depending on what is available. This option goes to the biggest pool of nodes. To get a more optimised run on Sandybridge or Ivybridge you should be using a modulefile with ‘avx’ in the name and using the instructions below.

Multi-threaded double-precision, AVX on Sandybridge nodes, 2 to 12 cores

An example batch submission script to run the double-precision mdrun_d executable with 8 threads:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 8
#$ -l sandybridge               # Force use of sandybridge nodes

export OMP_NUM_THREADS=$NSLOTS
mdrun_d
  #
  # This is the old naming convention (it will still work in this release)
  # The new gromacs convention is to run: gmx_d mdrun

Submit with the command: qsub scriptname

Multi-threaded single-precision, AVX on Ivybridge nodes, 2 to 16 cores

Note that GROMACS v5.1.4 (unlike v4.5.4) does not support the -nt flag to set the number of threads when using the multithreaded OpenMP (non-MPI) version. Instead set the OMP_NUM_THREADS environment variable as shown below.

An example batch submission script to run the single-precision mdrun executable with 16 threads:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 16
#$ -l ivybridge                 # Force use of Ivybridge nodes

export OMP_NUM_THREADS=$NSLOTS
mdrun

Submit with the command: qsub scriptname

Multi-threaded single-precision, AVX2 on Haswell nodes, 2 to 24 cores

Note that GROMACS v5.1.4 (unlike v4.5.4) does not support the -nt flag to set the number of threads when using the multithreaded OpenMP (non-MPI) version. Instead set the OMP_NUM_THREADS environment variable as shown below.

An example batch submission script to run the single-precision mdrun executable with 16 threads:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 24
#$ -l haswell                  # Force use of Haswell nodes

export OMP_NUM_THREADS=$NSLOTS
mdrun

Submit with the command: qsub scriptname

Single precision MPI (single-node), 2 to 24 cores

An example batch submission script to run the double-precision mdrun_mpi executable on 8 cores using mpi:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 8            
                                          
mpirun -n $NSLOTS mdrun_mpi

Submit with the command: qsub scriptname

Double precision MPI (single-node), 2 to 24 cores

An example batch submission script to run the double-precision mdrun_mpi_d executable on 8 cores using mpi:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 4             
                                          
mpirun -n $NSLOTS mdrun_mpi_d
  #
  # This is the old naming convention (it will still work in this release)
  # The new gromacs convention is to run: mpirun -n $NSLOTS gmx_mpi_d mdrun

Submit with the command: qsub scriptname

Single-precision AVX2, 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 (48 cores on two 24-core nodes) with the orte-24-ib.pe parallel environment (Intel Haswell nodes using infiniband):

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe orte-24-ib.pe 48           # EG: Two 24-core Intel Haswell nodes

mpirun -n $NSLOTS mdrun_mpi
  #
  # This is the old naming convention (it will still work in this release)
  # The new gromacs convention is to run: mpirun -n $NSLOTS gmx_mpi mdrun

Submit with the command: qsub scriptname

Illegal instruction

If during a batch job you try to run gromacs and get the following error:

Illegal instruction

This is because you have an AVX or AVX2 only version of the modulefile loaded which is not compatible with the compute nodes on which your job is running. Ensure your jobscript requests the correct type of compute node.

Error about OpenMP and cut-off scheme

If you encounter the following error:

OpenMP threads have been requested with cut-off scheme Group, but these 
are only supported with cut-off scheme Verlet

then please try using the mpi version of the software. Note that is is possible to run mpi versions on a single node (example above).

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

Sep 2017 – 5.1.4 installed with AVX support (GPU support with Intel compiler not possible)
Apr 2015 – 5.0.4 installed with AVX support (GPU support with Intel compiler not possible)
Dec 2014 – 4.6.7 installed with AVX support (specific user request for this) and documentation written.
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.