mdrun_mpi - performs a simulation, do a normal mode analysis or an
energy minimization across multiple CPUs or systems
mdrun_mpi -s topol.tpr -o traj.trr -x traj.xtc -cpi state.cpt -cpo
state.cpt -c confout.gro -e ener.edr -g md.log -dhdl dhdl.xvg -field
field.xvg -table table.xvg -tablep tablep.xvg -tableb table.xvg -rerun
rerun.xtc -tpi tpi.xvg -tpid tpidist.xvg -ei sam.edi -eo sam.edo -j
wham.gct -jo bam.gct -ffout gct.xvg -devout deviatie.xvg -runav
runaver.xvg -px pullx.xvg -pf pullf.xvg -mtx nm.mtx -dn dipole.ndx
-[no]h -[no]version -nice int -deffnm string -xvg enum -[no]pd -dd
vector -nt int -npme int -ddorder enum -[no]ddcheck -rdd real -rcon
real -dlb enum -dds real -gcom int -[no]v -[no]compact -[no]seppot
-pforce real -[no]reprod -cpt real -[no]cpnum -[no]append -maxh real
-multi int -replex int -reseed int -[no]ionize
The mdrun program is the main computational chemistry engine within
GROMACS. Obviously, it performs Molecular Dynamics simulations, but it
can also perform Stochastic Dynamics, Energy Minimization, test
particle insertion or (re)calculation of energies. Normal mode
analysis is another option. In this case mdrun builds a Hessian matrix
from single conformation. For usual Normal Modes-like calculations,
make sure that the structure provided is properly energy-minimized.
The generated matrix can be diagonalized by g_nmeig.
This version of the program will only run while using the OpenMPI
parallel computing library. See mpirun(1). Use the normal mdrun(1)
program for conventional single-threaded operations.
The mdrun program reads the run input file ( -s) and distributes the
topology over nodes if needed. mdrun produces at least four output
files. A single log file ( -g) is written, unless the option -seppot
is used, in which case each node writes a log file. The trajectory
file ( -o), contains coordinates, velocities and optionally forces.
The structure file ( -c) contains the coordinates and velocities of the
last step. The energy file ( -e) contains energies, the temperature,
pressure, etc, a lot of these things are also printed in the log file.
Optionally coordinates can be written to a compressed trajectory file (
The option -dhdl is only used when free energy calculation is turned
When mdrun is started using MPI with more than 1 node, parallelization
is used. By default domain decomposition is used, unless the -pd
option is set, which selects particle decomposition.
With domain decomposition, the spatial decomposition can be set with
option -dd. By default mdrun selects a good decomposition. The user
only needs to change this when the system is very inhomogeneous.
Dynamic load balancing is set with the option -dlb, which can give a
significant performance improvement, especially for inhomogeneous
systems. The only disadvantage of dynamic load balancing is that runs
are no longer binary reproducible, but in most cases this is not
important. By default the dynamic load balancing is automatically
turned on when the measured performance loss due to load imbalance is
5% or more. At low parallelization these are the only important
options for domain decomposition. At high parallelization the options
in the next two sections could be important for increasing the
When PME is used with domain decomposition, separate nodes can be
assigned to do only the PME mesh calculation; this is computationally
more efficient starting at about 12 nodes. The number of PME nodes is
set with option -npme, this can not be more than half of the nodes.
By default mdrun makes a guess for the number of PME nodes when the
number of nodes is larger than 11 or performance wise not compatible
with the PME grid x dimension. But the user should optimize npme.
Performance statistics on this issue are written at the end of the log
file. For good load balancing at high parallelization, the PME grid x
and y dimensions should be divisible by the number of PME nodes (the
simulation will run correctly also when this is not the case).
This section lists all options that affect the domain decomposition.
Option -rdd can be used to set the required maximum distance for inter
charge-group bonded interactions. Communication for two-body bonded
interactions below the non-bonded cut-off distance always comes for
free with the non-bonded communication. Atoms beyond the non-bonded
cut-off are only communicated when they have missing bonded
interactions; this means that the extra cost is minor and nearly
indepedent of the value of -rdd. With dynamic load balancing option
-rdd also sets the lower limit for the domain decomposition cell sizes.
By default -rdd is determined by mdrun based on the initial
coordinates. The chosen value will be a balance between interaction
range and communication cost.
When inter charge-group bonded interactions are beyond the bonded
cut-off distance, mdrun terminates with an error message. For pair
interactions and tabulated bonds that do not generate exclusions, this
check can be turned off with the option -noddcheck.
When constraints are present, option -rcon influences the cell size
limit as well. Atoms connected by NC constraints, where NC is the
LINCS order plus 1, should not be beyond the smallest cell size. A
error message is generated when this happens and the user should change
the decomposition or decrease the LINCS order and increase the number
of LINCS iterations. By default mdrun estimates the minimum cell size
required for P-LINCS in a conservative fashion. For high
parallelization it can be useful to set the distance required for
P-LINCS with the option -rcon.
The -dds option sets the minimum allowed x, y and/or z scaling of the
cells with dynamic load balancing. mdrun will ensure that the cells can
scale down by at least this factor. This option is used for the
automated spatial decomposition (when not using -dd) as well as for
determining the number of grid pulses, which in turn sets the minimum
allowed cell size. Under certain circumstances the value of -dds might
need to be adjusted to account for high or low spatial inhomogeneity of
The option -gcom can be used to only do global communication every n
steps. This can improve performance for highly parallel simulations
where this global communication step becomes the bottleneck. For a
global thermostat and/or barostat the temperature and/or pressure will
also only be updated every -gcom steps. By default it is set to the
minimum of nstcalcenergy and nstlist.
With -rerun an input trajectory can be given for which forces and
energies will be (re)calculated. Neighbor searching will be performed
for every frame, unless nstlist is zero (see the .mdp file).
ED (essential dynamics) sampling is switched on by using the -ei flag
followed by an .edi file. The .edi file can be produced using
options in the essdyn menu of the WHAT IF program. mdrun produces a
.edo file that contains projections of positions, velocities and forces
onto selected eigenvectors.
When user-defined potential functions have been selected in the .mdp
file the -table option is used to pass mdrun a formatted table with
potential functions. The file is read from either the current directory
or from the GMXLIB directory. A number of pre-formatted tables are
presented in the GMXLIB dir, for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard
Jones potentials with normal Coulomb. When pair interactions are
present a separate table for pair interaction functions is read using
the -tablep option.
When tabulated bonded functions are present in the topology,
interaction functions are read using the -tableb option. For each
different tabulated interaction type the table file name is modified in
a different way: before the file extension an underscore is appended,
then a b for bonds, an a for angles or a d for dihedrals and finally
the table number of the interaction type.
The options -px and -pf are used for writing pull COM coordinates and
forces when pulling is selected in the .mdp file.
With -multi multiple systems are simulated in parallel. As many input
files are required as the number of systems. The system number is
appended to the run input and each output filename, for instance
topol.tpr becomes topol0.tpr, topol1.tpr etc. The number of nodes per
system is the total number of nodes divided by the number of systems.
One use of this option is for NMR refinement: when distance or
orientation restraints are present these can be ensemble averaged over
all the systems.
With -replex replica exchange is attempted every given number of
steps. The number of replicas is set with the -multi option, see
above. All run input files should use a different coupling
temperature, the order of the files is not important. The random seed
is set with -reseed. The velocities are scaled and neighbor searching
is performed after every exchange.
Finally some experimental algorithms can be tested when the appropriate
options have been given. Currently under investigation are:
polarizability, and X-Ray bombardments.
The option -pforce is useful when you suspect a simulation crashes due
to too large forces. With this option coordinates and forces of atoms
with a force larger than a certain value will be printed to stderr.
Checkpoints containing the complete state of the system are written at
regular intervals (option -cpt) to the file -cpo, unless option -cpt
is set to -1. The previous checkpoint is backed up to state_prev.cpt
to make sure that a recent state of the system is always available,
even when the simulation is terminated while writing a checkpoint.
With -cpnum all checkpoint files are kept and appended with the step
number. A simulation can be continued by reading the full state from
file with option -cpi. This option is intelligent in the way that if
no checkpoint file is found, Gromacs just assumes a normal run and
starts from the first step of the tpr file. By default the output will
be appending to the existing output files. The checkpoint file contains
checksums of all output files, such that you will never loose data when
some output files are modified, corrupt or removed. There are three
scenarios with -cpi:
* no files with matching names are present: new output files are
* all files are present with names and checksums matching those stored
in the checkpoint file: files are appended
* otherwise no files are modified and a fatal error is generated
With -noappend new output files are opened and the simulation part
number is added to all output file names. Note that in all cases the
checkpoint file itself is not renamed and will be overwritten, unless
its name does not match the -cpo option.
With checkpointing the output is appended to previously written output
files, unless -noappend is used or none of the previous output files
are present (except for the checkpoint file). The integrity of the
files to be appended is verified using checksums which are stored in
the checkpoint file. This ensures that output can not be mixed up or
corrupted due to file appending. When only some of the previous output
files are present, a fatal error is generated and no old output files
are modified and no new output files are opened. The result with
appending will be the same as from a single run. The contents will be
binary identical, unless you use a different number of nodes or dynamic
load balancing or the FFT library uses optimizations through timing.
With option -maxh a simulation is terminated and a checkpoint file is
written at the first neighbor search step where the run time exceeds
When mdrun receives a TERM signal, it will set nsteps to the current
step plus one. When mdrun receives an INT signal (e.g. when ctrl+C is
pressed), it will stop after the next neighbor search step (with
nstlist=0 at the next step). In both cases all the usual output will
be written to file. When running with MPI, a signal to one of the
mdrun processes is sufficient, this signal should not be sent to mpirun
or the mdrun process that is the parent of the others.
When mdrun is started with MPI, it does not run niced by default.
-s topol.tpr Input
Run input file: tpr tpb tpa
-o traj.trr Output
Full precision trajectory: trr trj cpt
-x traj.xtc Output, Opt.
Compressed trajectory (portable xdr format)
-cpi state.cpt Input, Opt.
-cpo state.cpt Output, Opt.
-c confout.gro Output
Structure file: gro g96 pdb etc.
-e ener.edr Output
-g md.log Output
-dhdl dhdl.xvg Output, Opt.
-field field.xvg Output, Opt.
-table table.xvg Input, Opt.
-tablep tablep.xvg Input, Opt.
-tableb table.xvg Input, Opt.
-rerun rerun.xtc Input, Opt.
Trajectory: xtc trr trj gro g96 pdb cpt
-tpi tpi.xvg Output, Opt.
-tpid tpidist.xvg Output, Opt.
-ei sam.edi Input, Opt.
ED sampling input
-eo sam.edo Output, Opt.
ED sampling output
-j wham.gct Input, Opt.
General coupling stuff
-jo bam.gct Output, Opt.
General coupling stuff
-ffout gct.xvg Output, Opt.
-devout deviatie.xvg Output, Opt.
-runav runaver.xvg Output, Opt.
-px pullx.xvg Output, Opt.
-pf pullf.xvg Output, Opt.
-mtx nm.mtx Output, Opt.
-dn dipole.ndx Output, Opt.
Print help info and quit
Print version info and quit
-nice int 0
Set the nicelevel
Set the default filename for all file options
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
Use particle decompostion
-dd vector 0 0 0
Domain decomposition grid, 0 is optimize
-nt int 0
Number of threads to start (0 is guess)
-npme int -1
Number of separate nodes to be used for PME, -1 is guess
-ddorder enum interleave
DD node order: interleave, pp_pme or cartesian
Check for all bonded interactions with DD
-rdd real 0
The maximum distance for bonded interactions with DD (nm), 0 is
determine from initial coordinates
-rcon real 0
Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto
Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8
Minimum allowed dlb scaling of the DD cell size
-gcom int -1
Global communication frequency
Be loud and noisy
Write a compact log file
Write separate V and dVdl terms for each interaction type and node to
the log file(s)
-pforce real -1
Print all forces larger than this (kJ/mol nm)
Try to avoid optimizations that affect binary reproducibility
-cpt real 15
Checkpoint interval (minutes)
Keep and number checkpoint files
Append to previous output files when continuing from checkpoint
instead of adding the simulation part number to all file names
-maxh real -1
Terminate after 0.99 times this time (hours)
-multi int 0
Do multiple simulations in parallel
-replex int 0
Attempt replica exchange every steps
-reseed int -1
Seed for replica exchange, -1 is generate a seed
Do a simulation including the effect of an X-Ray bombardment on your
More information about GROMACS is available at
Thu 26 Aug 2010 mdrun_mpi(1)