NAME
mdrun - performs a simulation, do a normal mode analysis or an energy
minimization
VERSION 4.0.1
SYNOPSIS
mdrun -s topol.tpr -o traj.trr -x traj.xtc -cpi state.cpt -cpo
state.cpt -c confout.gro -e ener.edr -g md.log -dgdl dgdl.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 -nice int -deffnm string -[no]xvgr -[no]pd -dd vector -npme int
-ddorder enum -[no]ddcheck -rdd real -rcon real -dlb enum -dds real
-[no]sum -[no]v -[no]compact -[no]seppot -pforce real -[no]reprod -cpt
real -[no]append -maxh real -multi int -replex int -reseed int
-[no]glas -[no]ionize
DESCRIPTION
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.
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 (
-x).
The option -dgdl is only used when free energy perturbation is turned
on.
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
performace.
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, npme should be
divisible by the number of PME nodes
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 system.
The option -nosum can be used to only sum the energies at every
neighbor search step and energy output step. 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 nstlist steps. With this option the energy file will not
contain averages and fluctuations over all integration steps.
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 -pi, -po, -pd, -pn are used for potential of mean force
calculations and umbrella sampling. See manual.
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, glass simulations 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. 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.
With checkpointing you can also use the option -append to just
continue writing to the previous output files. This is not enabled by
default since it is potentially dangerous if you move files, but if you
just leave all your files in place and restart mdrun with exactly the
same command (with options -cpi and -append) the result will be the
same as from a single run. The contents will be binary identical
(unless you use dynamic load balancing), but for technical reasons
there might be some extra energy frames when using checkpointing
(necessary for restarts without appending).
With option -maxh a simulation is terminated and a checkpoint file is
written at the first neighbor search step where the run time exceeds
-maxh*0.99 hours.
When mdrun receives a TERM signal, it will set nsteps to the current
step plus one. When mdrun receives a USR1 signal, 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.
FILES
-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.
Checkpoint file
-cpo state.cpt Output, Opt.
Checkpoint file
-c confout.gro Output
Structure file: gro g96 pdb
-e ener.edr Output
Energy file: edr ene
-g md.log Output
Log file
-dgdl dgdl.xvg Output, Opt.
xvgr/xmgr file
-field field.xvg Output, Opt.
xvgr/xmgr file
-table table.xvg Input, Opt.
xvgr/xmgr file
-tablep tablep.xvg Input, Opt.
xvgr/xmgr file
-tableb table.xvg Input, Opt.
xvgr/xmgr file
-rerun rerun.xtc Input, Opt.
Trajectory: xtc trr trj gro g96 pdb cpt
-tpi tpi.xvg Output, Opt.
xvgr/xmgr file
-tpid tpidist.xvg Output, Opt.
xvgr/xmgr file
-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.
xvgr/xmgr file
-devout deviatie.xvg Output, Opt.
xvgr/xmgr file
-runav runaver.xvg Output, Opt.
xvgr/xmgr file
-px pullx.xvg Output, Opt.
xvgr/xmgr file
-pf pullf.xvg Output, Opt.
xvgr/xmgr file
-mtx nm.mtx Output, Opt.
Hessian matrix
-dn dipole.ndx Output, Opt.
Index file
OTHER OPTIONS
-[no]hno
Print help info and quit
-nice int 19
Set the nicelevel
-deffnm string
Set the default filename for all file options
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-[no]pdno
Use particle decompostion
-dd vector 0 0 0
Domain decomposition grid, 0 is optimize
-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
-[no]ddcheckyes
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
-[no]sumyes
Sum the energies at every step
-[no]vno
Be loud and noisy
-[no]compactyes
Write a compact log file
-[no]seppotno
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)
-[no]reprodno
Try to avoid optimizations that affect binary reproducibility
-cpt real 15
Checkpoint interval (minutes)
-[no]appendno
Append to previous output files when restarting from checkpoint
-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
-[no]glasno
Do glass simulation with special long range corrections
-[no]ionizeno
Do a simulation including the effect of an X-Ray bombardment on your
system
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 mdrun(1)