GROMACS

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According to the
official website
, GROMACS is:
a versatile package to perform
molecular dynamics
, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
Note
GROMACS should not be used as a
black box
. The user is strongly encouraged to read and study the
scientific papers
related to the methods and force fields that are employed by GROMACS.
Installation
Install
the
gromacs
AUR
package. Be sure to
edit
the
PKGBUILD
to suit your system (i.e. for MPI or GPU support). Some of the
CMake
options you may want to add/modify in the PKGBUILD are (cf.
the latest GROMACS installation guide
):
-DGMX_DOUBLE=ON
- Add if you need
double precision
. According to the GROMACS install guide, double precision is "slower, and not normally useful." If you set this flag, the default suffix for all GROMACS programs is set to
_d
.
-DGMX_GPU=value
, where
value
is one of
CUDA, OpenCL, SYCL, HIP
- Add in order to build with
GPGPU
support. Several other flags may be necessary; refer to the latest GROMACS installation guide.
-DGMX_MPI=ON
- Add to create a build able to run across multiple compute nodes. You will also need to have an
MPI
library such as
openmpi
or
mpich
AUR
. If you do not need MPI support (
i.e.
, you just run on a single computer), you do not need this flag. If you set this flag, the default suffix for all GROMACS programs is set to
_mpi
.
-DGMX_SIMD=
xxx
- GROMACS should detect the best
SIMD
instructions for your processor, so this flag should not be needed. But if you have some kind of compilation error, you can specify the SIMD level here. A list of available options for
xxx
is listed in the latest GROMACS installation guide.
Note
If you are compiling on a Haswell processor, you may need to configure
makepkg
to use
-march=native
to successfully compile with AVX2_256 instructions.
-DGMX_X11=ON
- Set to use
gmx view
, the built-in trajectory viewer. This flag requires the
openmotif
and
libx11
packages.
-DREGRESSIONTEST_DOWNLOAD=ON
- Set to test your GROMACS build. To run the tests
set your build to run
make check
. The
libxml2
package is required.
-DGMX_DEFAULT_SUFFIX=OFF
- Set to turn of default suffix for GROMACS programs for MPI or double precision builds.
-DGMX_BINARY_SUFFIX=
xxx
and
-DGMX_LIBS_SUFFIX=
xxx
- Set the default suffix to
xxx
for binaries and libraries, respectively.
Some other packages that may increase performance are:
boost-libs
- An external
Boost library
can be used to provide better implementation support for smart pointers and exception handling.
hwloc
- Run-time detection of hardware capabilities can be improved by linking with hwloc
lapack
- Hardware-optimized BLAS and LAPACK libraries are useful for a few of the GROMACS utilities focused on normal modes and matrix manipulation, but they do not provide any benefits for normal simulations.
Since
version 2019
, GROMACS build is
reproducible
.
Configuration
By default the top-level force field directory is located at
/usr/share/gromacs/top
. This can be changed by setting a different directory to the
GMXLIB
environment variable
. This is useful if you make modifications to a force field, or if you have another set of force fields you would like to use.
Usage
Below is a basic workflow with most of the major commands mentioned. Every command should begin with
gmx
. For more details on using GROMACS
find a good tutorial and read the manual
. A helpful flow chart is
here
.
Tip
Each command has its own
man page
, with a hyphen substituted for the space in between
gmx
and the command. For example, the man page for
gmx pdb2gmx
is located at
gmx-pdb2gmx
.
Setup
Simulations require a structure file (
.gro
/
.pdb
), a topology file (
.top
), and a parameters file (
.mdp
). The following steps illustrate how to obtain these.
Obtain structure file
A structure file, which contains the coordinates of all particles, can be obtained from a
protein database
or created by the user using a
program
.
Tip
One can use any structure file format (
e.g
, the
PDB file format
) with most GROMACS programs, not just the
GROMACS format
.
Generate a topology
A topology file indicates how atomic particles interact with one another. One method for generating a topology file is to use
gmx pdb2gmx
. If your solute is in a file named
protein.pdb
, do the following:
$ gmx pdb2gmx -f protein.pdb
Then you will be prompted to select a
force field
and
water model
. A new structure file in gro format will be generated (
conf.gro
) as well as the corresponding topology file (
topol.top
).
If you did not obtain your structure file from a protein database, but instead created it yourself, most likely you will need to create a residue template file (
.rtp
) for your molecule as well as update the
.pdb
file. An example
.rtp
file for OPLS methane is found
here
with its corresponding
.pdb
file
here
(both files are from James Barnett's
tutorial
). The
.rtp
file must be placed in the force field directory for the force field you are going to use.
See below
for alternative ways to generate or obtain topologies.
Box creation
A quick way to create a simulation box full of water around a solute is to do:
$ gmx solvate -cp conf.gro -cs
water
-box
X
Y
Z
-o conf.gro -p topol.top
In the above the solute/protein's coordinates are initially stored in
conf.gro
. A water model using
water
.gro (either found in the top-level force field directory or the current one) is used to fill the box with solvent, and the box dimensions are
X
,
Y
, and
Z
. The topology file,
topol.top
is updated and the new system is output to
conf.gro
.
If
-cs
is omitted, a three-point water model is used. The other available water structures are
tip4p
and
tip5p
.
Note
tip4p
is simply a set of four-point water model coordinates and can correspond to any four-point water model, not just
TIP4P
.
You can also
use different box types
and
non-water solvents
.
Adding ions
If the system is not charge-neutral, ions should generally be added. For example if the net charge of your system is -2, to add two positive sodium ions do:
$ gmx grompp -f grompp.mdp
$ gmx genion -s topol.tpr -np 2 -pname Na -o conf.gro -p topol.top
Then select the index group corresponding with the solvent, which will be replaced by the ions. The
-nname
argument should correspond to an ion in the force field you are using.
Tip
The
.mdp
file does not need to correspond to any particular simulation step. It is only used to generate the
.tpr
file for
gmx genion
.
Parameter files
A parameters file should be created for each different step of a set of simulations (
e.g.
, minimization, equilibration, production). A list of all possible options is
here
.
Here is a sample parameter file for a ten second production run at standard conditions:
dt                       = 0.002
nsteps                   = 5000000

nstxout-compressed       = 2500

coulombtype              = PME
rcoulomb                 = 1.0

vdwtype                  = Cut-off
rvdw                     = 1.0
DispCorr                 = EnerPres

tcoupl                   = Nose-Hoover
nh-chain-length          = 1
tc-grps                  = System
tau-t                    = 2.0
ref-t                    = 298.15

pcoupl                   = Parrinello-Rahman 
tau_p                    = 2.0
compressibility          = 4.46e-5
ref_p                    = 1.0 

constraints              = h-bonds
continuation             = yes
Tip
A commented parameters file with all options (even those not explicitly listed in your file) is output when running
gmx grompp
and saved by default as
mdout.mdp
.
Running
Basics
Simulations typically consist of two parts, described below.
First, there is a preprocessing step where the structure file, topology file, and parameters file are read in and written out to a single
.tpr
file, also sometimes referred to as a topology file:
$ gmx grompp -f grompp.mdp -c conf.gro -p topol.top -o topol.tpr
Here
grompp.mdp
is the parameters file for this simulation step,
conf.gro
is the structure file that begins this simulation step, and
topol.top
is the topology file. A structure file (
.gro
) is output at the end of every simulation, so it should be used with
-c
in a simulation that continues from the previous one (
e.g.
, an initial equilibration run should use the structure file output from a previous minimization step).
Note
When a checkpoint file is available, you should prefer to read in it with the
-t
flag (instead of just a structure file with
-c
), since it contains additional information. When using both the
-c
and
-t
flags
gmx grompp
checks for the checkpoint file first, and if it is not found, then falls back to the structure file indicated. If a structure file is not indicated  in this case, the default filename
conf.gro
is used.
Next, there is the actual simulation. The
.tpr
file is read in with the main program
gmx mdrun
to run the simulation:
$ gmx mdrun -s topol.tpr
Tip
gmx mdrun
outputs several files. To make them have the same prefix use the
-deffnm
flag.
In general these two parts are repeated for an energy minimization step, an equilibration step, and a production step. Multiple equilibration steps may be needed, especially when turning on pressure coupling. The production step and the last equilibration step should use the exact same parameters (
.mdp
) except for the length of the simulation.
As an example, a set of simulations consisting of one minimization step, one equilbration step, and one production step might look like this:
#!/bin/sh

gmx grompp -f min.mdp -o min.tpr -c conf.gro -p topol.top
gmx mdrun -deffnm min

gmx grompp -f eql.mdp -o eql.tpr -c min.gro -p topol.top
gmx mdrun -deffnm eql

gmx grompp -f prd.mdp -o prd.tpr -t eql.cpt -p topol.top
gmx mdrun -deffnm prd
Here
min.mdp
,
eql.mdp
, and
prd.mdp
are parameter files for the minimization, equilibration, and production steps, respectively.
Acceleration & Parallelization
By default GROMACS uses all available processors on a single node. To run across multiple nodes, an MPI library is required. Using openmpi to run GROMACS takes the following form:
$ mpirun -np
totalranks
-npernode
rankspernode
--hostfile
filename
gmx mdrun -s topol.tpr
Here
totalranks
is the total number of MPI ranks to create,
rankspernode
is the number of MPI ranks per node, and
filename
is the hostfile used to determine on which hosts to run the processes.
OpenMPI be used together with OpenMP as seen here:
$ mpirun -np
totalranks
-npernode
rankspernode
--hostfile
filename
gmx mdrun -ntomp
openmpthreads
-s topol.tpr
If compiled without an external MPI library one can control MPI ranks and OMP threads, using GROMAC's thread-MPI. This will not be able to be run across multiple compute nodes:
$ gmx mdrun -ntmpi
totalranks
-ntomp
openmpthreads
-s topol.tpr
Here
openmpthreads
is the number of OpenMP threads to create.
totalranks
*
openmpthreads
should equal the total number of processors.
Tip
Splitting up a simulation between MPI ranks and OMP threads is generally slower than using one or the other.
GROMACS automatically detects any available GPUs if it was compiled with GPU support. The number of MPI ranks must be a multiple of the number of GPUs to be used. Using a GPU requires the
Verlet
cut-off scheme, which is
set
with the parameter
cutoff-scheme
in your
.mdp
file. The command takes the basic form:
$ mpirun -np
totalranks
-npernode
rankspernode
--hostfile
filename
gmx mdrun -ntomp
openmpthreads
-s topol.tpr -gpu_id
gpuids
Here
gpuids
is the zero-based id of each GPU in a list. That is, with only one GPU (
-np 1
), you would use
-gp_uid 0
. If two GPUs are available (
-np 2
), you would use
-gpu_id 01
. To use a GPU on multiple MPI ranks, simply list its id the number of times to be used. For example, to use four MPI ranks on two GPUS one would use
-np 4
, and
-gpu_id 0011
, thus using each GPU on two MPI ranks. If running on two twenty-core machines, the command would look like:
$ mpirun -np 8 -npernode 4 --hostfile
filename
gmx mdrun -ntomp 5 -s topol.tpr -gpu_id 0011
If using GROMACS thread-MPI on one twenty core machine this would be:
$ gmx mdrun -ntmpi 4 -ntomp 5 -s topol.tpr -gpu_id 0011
Tip
Running multiple simulations on a GPU can be more efficient than running them separately. To do so use the
-multi
or
-multidir
flag.
See
mpirun(1)
as well as the
GROMACS section on MPI acceleration and parallelization for more options
.
Restart a simulation
To restart a simulation from a checkpoint file do:
$ gmx mdrun -s topol.tpr -cpi state.cpt
Here
topol.tpr
is the original
.tpr
used in the simulation, and
state.cpt
is the last checkpoint file from that simulation.
Extend a simulation
To extend a simulation create a modified
.tpr
file and use it with
gmx mdrun
:
$ gmx convert-tpr -s topol.tpr -extend
time
-o tpxout.tpr
$ gmx mdrun -s tpxout.tpr -cpi state.cpt
Where
time
is how much longer to run the simulation in picoseconds,
topol.tpr
is the
.tpr
file associated with the original simulation, and
state.cpt
is the latest checkpoint file from that simulation. Instead of using
-extend
one can also use
-until
to specify the absolute ending time in picoseconds.
Analysis
Tools
GROMACS comes with many analysis tools built-in. A list of all possible possible commands can be obtained by typing
gmx help commands
or by opening the man page for
gromacs
.
Some of the more prominent analysis commands are:
gmx bar
—
calculate free energy difference estimates through
Bennett's acceptance ratio
.
gmx energy
—
writes energies to xvg files and display averages.
gmx rdf
—
calculate
radial distribution functions
.
gmx trjconv
—
convert and manipulates trajectory files.
gmx wham
—
Perform weighted histogram analysis after
umbrella sampling
.
See below
for other available tools.
Index Files
Index files are optionally used in almost all GROMACS analysis programs. The program
gmx make_ndx
controls the creation and modification of index files. Index files consist of group names and integer indices indicating the location of atomic sites in a trajectory frame. They are only required if the available residues found in a structure file do not group atomic sites together in the desired way. When running
gmx make_ndx
the user is presented with a prompt in order to select, combine, and split groups of atoms through various commands. Typing
h
at the make_ndx prompt gives a full description of the commands available.
Development
GROMACS uses
Git
for version control, so familiarize yourself with its usage, especially the topic on
collaboration
. To begin
contributing
you need to have a
GitLab
account with an
SSH key
. The official repository is located at
gromacs/gromacs
and it can be forked. Changes should be submitted as
merge requests
. When making changes, follow
the style guidelines
for the code and commits.
When you are ready to share your changes, ensure your HEAD is up to date with a branch that you want to contribute to. In general three branches are used:
main
is used for long-term development of major features which may require large changes in code.
release-
x
-
y is for features that do not require as much code change, where
x
and
y
are the major and minor version numbers of the next release respectively.
release-
x
-
y
-patches
is for bug fixes and small documentation changes to a previous release.
Tips and tricks
Create non-cubic box and fill with solvent
To create a non-cubic box filled with solvent, first do:
$ gmx editconf -f
protein
.pdb -bt
boxtype
-d
dist
-o box.gro
The above command creates a
boxtype
box around the molecule in
protein
.pdb
at
dist
nm in every direction. The box is saved as
box.gro
.
boxtype
can be
triclinic
,
cubic
,
dodecahedron
, or
octahedron
.
Then fill with solvent:
$ gmx solvate -cs tip4p -cp box.gro -o conf.gro -p topol.top
Use multiple solutes
If you want to use multiple solutes randomly inserted, first do:
$ gmx insert-molecules -box
X
Y
Z
-ci solute.pdb -nmol
N
-o box.gro
Where
X
,
Y
, and
Z
are the box dimensions in nanometers, and
N
is the number to insert. You will need to update your topology file with the inserted number of molecules.
Then fill with solvent:
$ gmx solvate -cs tip4p -cp box.gro -o conf.gro -p topol.top
Note
When using a visualization program you will see a triclinic box, since all non-cubic boxes are ultimately represented in GROMACS as a triclinic box.
Use a non-water solvent
To use a non-water solvent with standard tools such as
gmx pdb2gmx
and
gmx solvate
do the following:
Create one solvent molecule's structure file and topology.
Create a box containing a couple hundred of the solvent molecules (216 seems to be a standard) and run a short equilibration on the system at standard conditions.
Copy the output structure file
.gro
from the simulation to
solvent
.gro
, where
solvent
is the name you wish to use for this molecule. Place this copy in the top level force field directory (where each force field has its own directory).
Modify the topology file for the single solvent by removing everything but the
[moleculetype]
section and name the molecule in the file as
SOL
.
Rename the topology file as
solvent
.itp
and move it to the force field directory to which it applies.
Update
watermodels.dat
for the force field you wish to use with this solvent (located in the force field's directory), adding the solvent. You will simply add a line with
filename
shortdescription
longdescription
where
filename
omits the file extension.
Now when you run
gmx pdb2gmx
this solvent model should be available for the applicable force field. Additionally you can use
-cs
solvent
when running
gmx solvate
.
See also
Structure and topology databases
Automated Topology Builder & Repository
—
repository for building blocks and interaction parameter files for molecules
as well as
an automated builder to help generate building blocks for novel molecules.
RCSB Protein Data Bank
—
information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.
SwissParam
—
provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS.
TraPPE Parameter Database
— search by molecule name, or build your own, in order to obtain TraPPE force field parameters. Note that it is necessary to convert the parameters to the correct units.
Virtual Chemistry
— comparison of experimental and computational results for thousands of molecules. Contains validated topology input files for CGenFF, GAFF and OPLS/AA.
External libraries and programs
See
List of applications/Science#Chemistry
.
Development
GROMACS Issues on GitLab
— project management page, where bugs, issues, and features are reported and tracked.
GROMACS Merge requests on GitLab
— the project's code review system.
Documentation
GROMACS forums
— very active forums for users seeking help. Make sure to read the manual and search the archive before posting.
GROMACS Manual
— official GROMACS manual for the current version.
GROMACS Online Reference
Tutorials
Official GROMACS Tutorials
Justin Lemkul's Tutorials
— includes a variety of different simulation methods (umbrella sampling, free energy calculations, etc).
James Barnett's Tutorials
— a few basic tutorials on simulations with an organic solute. Includes how to use
gmx pdb2gmx
with a user-created molecule.