Provided by: gromacs-data_5.1.2-1ubuntu1_all 
NAME
gmx-mdrun - Perform a simulation, do a normal mode analysis or an energy minimization
SYNOPSIS
gmx mdrun [-s [<.tpr>]] [-cpi [<.cpt>]] [-table [<.xvg>]]
[-tabletf [<.xvg>]] [-tablep [<.xvg>]] [-tableb [<.xvg>]]
[-rerun [<.xtc/.trr/...>]] [-ei [<.edi>]]
[-multidir [<dir> [...]]] [-membed [<.dat>]] [-mp [<.top>]]
[-mn [<.ndx>]] [-o [<.trr/.cpt/...>]] [-x [<.xtc/.tng>]]
[-cpo [<.cpt>]] [-c [<.gro/.g96/...>]] [-e [<.edr>]]
[-g [<.log>]] [-dhdl [<.xvg>]] [-field [<.xvg>]]
[-tpi [<.xvg>]] [-tpid [<.xvg>]] [-eo [<.xvg>]]
[-devout [<.xvg>]] [-runav [<.xvg>]] [-px [<.xvg>]]
[-pf [<.xvg>]] [-ro [<.xvg>]] [-ra [<.log>]] [-rs [<.log>]]
[-rt [<.log>]] [-mtx [<.mtx>]] [-dn [<.ndx>]]
[-if [<.xvg>]] [-swap [<.xvg>]] [-deffnm <string>]
[-xvg <enum>] [-dd <vector>] [-ddorder <enum>]
[-npme <int>] [-nt <int>] [-ntmpi <int>] [-ntomp <int>]
[-ntomp_pme <int>] [-pin <enum>] [-pinoffset <int>]
[-pinstride <int>] [-gpu_id <string>] [-[no]ddcheck]
[-rdd <real>] [-rcon <real>] [-dlb <enum>] [-dds <real>]
[-gcom <int>] [-nb <enum>] [-nstlist <int>] [-[no]tunepme]
[-[no]v] [-[no]compact] [-pforce <real>] [-[no]reprod]
[-cpt <real>] [-[no]cpnum] [-[no]append] [-nsteps <int>]
[-maxh <real>] [-multi <int>] [-replex <int>] [-nex <int>]
[-reseed <int>]
DESCRIPTION
gmx mdrun 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
gmx nmeig.
The mdrun program reads the run input file (-s) and distributes the topology over ranks if needed. mdrun
produces at least four output files. A single log file (-g) is written. 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 -dhdl is only used when free energy calculation is turned on.
Running mdrun efficiently in parallel is a complex topic topic, many aspects of which are covered in the
online User Guide. You should look there for practical advice on using many of the options available in
mdrun.
ED (essential dynamics) sampling and/or additional flooding potentials are switched on by using the -ei
flag followed by an .edi file. The .edi file can be produced with the make_edi tool or by using options
in the essdyn menu of the WHAT IF program. mdrun produces a .xvg output 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.
Finally some experimental algorithms can be tested when the appropriate options have been given.
Currently under investigation are: polarizability.
The option -membed does what used to be g_membed, i.e. embed a protein into a membrane. This module
requires a number of settings that are provided in a data file that is the argument of this option. For
more details in membrane embedding, see the documentation in the user guide. The options -mn and -mp are
used to provide the index and topology files used for the embedding.
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 written
* 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 ranks 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 -maxh*0.99 hours. This option is particularly useful in
combination with setting nsteps to -1 either in the mdp or using the similarly named command line option.
This results in an infinite run, terminated only when the time limit set by -maxh is reached (if any)or
upon receiving a signal.
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 ranks is sufficient, this signal should not be sent to mpirun or
the mdrun process that is the parent of the others.
Interactive molecular dynamics (IMD) can be activated by using at least one of the three IMD switches:
The -imdterm switch allows one to terminate the simulation from the molecular viewer (e.g. VMD). With
-imdwait, mdrun pauses whenever no IMD client is connected. Pulling from the IMD remote can be turned on
by -imdpull. The port mdrun listens to can be altered by -imdport.The file pointed to by -if contains
atom indices and forces if IMD pulling is used.
When mdrun is started with MPI, it does not run niced by default.
OPTIONS
Options to specify input files:
-s [<.tpr>] (topol.tpr)
Portable xdr run input file
-cpi [<.cpt>] (state.cpt) (Optional)
Checkpoint file
-table [<.xvg>] (table.xvg) (Optional)
xvgr/xmgr file
-tabletf [<.xvg>] (tabletf.xvg) (Optional)
xvgr/xmgr file
-tablep [<.xvg>] (tablep.xvg) (Optional)
xvgr/xmgr file
-tableb [<.xvg>] (table.xvg) (Optional)
xvgr/xmgr file
-rerun [<.xtc/.trr/...>] (rerun.xtc) (Optional)
Trajectory: xtc trr cpt gro g96 pdb tng
-ei [<.edi>] (sam.edi) (Optional)
ED sampling input
-multidir [<dir> [...]] (rundir) (Optional)
Run directory
-membed [<.dat>] (membed.dat) (Optional)
Generic data file
-mp [<.top>] (membed.top) (Optional)
Topology file
-mn [<.ndx>] (membed.ndx) (Optional)
Index file
Options to specify output files:
-o [<.trr/.cpt/...>] (traj.trr)
Full precision trajectory: trr cpt tng
-x [<.xtc/.tng>] (traj_comp.xtc) (Optional)
Compressed trajectory (tng format or portable xdr format)
-cpo [<.cpt>] (state.cpt) (Optional)
Checkpoint file
-c [<.gro/.g96/...>] (confout.gro)
Structure file: gro g96 pdb brk ent esp
-e [<.edr>] (ener.edr)
Energy file
-g [<.log>] (md.log)
Log file
-dhdl [<.xvg>] (dhdl.xvg) (Optional)
xvgr/xmgr file
-field [<.xvg>] (field.xvg) (Optional)
xvgr/xmgr file
-tpi [<.xvg>] (tpi.xvg) (Optional)
xvgr/xmgr file
-tpid [<.xvg>] (tpidist.xvg) (Optional)
xvgr/xmgr file
-eo [<.xvg>] (edsam.xvg) (Optional)
xvgr/xmgr file
-devout [<.xvg>] (deviatie.xvg) (Optional)
xvgr/xmgr file
-runav [<.xvg>] (runaver.xvg) (Optional)
xvgr/xmgr file
-px [<.xvg>] (pullx.xvg) (Optional)
xvgr/xmgr file
-pf [<.xvg>] (pullf.xvg) (Optional)
xvgr/xmgr file
-ro [<.xvg>] (rotation.xvg) (Optional)
xvgr/xmgr file
-ra [<.log>] (rotangles.log) (Optional)
Log file
-rs [<.log>] (rotslabs.log) (Optional)
Log file
-rt [<.log>] (rottorque.log) (Optional)
Log file
-mtx [<.mtx>] (nm.mtx) (Optional)
Hessian matrix
-dn [<.ndx>] (dipole.ndx) (Optional)
Index file
-if [<.xvg>] (imdforces.xvg) (Optional)
xvgr/xmgr file
-swap [<.xvg>] (swapions.xvg) (Optional)
xvgr/xmgr file
Other options:
-deffnm <string>
Set the default filename for all file options
-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none
-dd <vector> (0 0 0)
Domain decomposition grid, 0 is optimize
-ddorder <enum> (interleave)
DD rank order: interleave, pp_pme, cartesian
-npme <int> (-1)
Number of separate ranks to be used for PME, -1 is guess
-nt <int> (0)
Total number of threads to start (0 is guess)
-ntmpi <int> (0)
Number of thread-MPI threads to start (0 is guess)
-ntomp <int> (0)
Number of OpenMP threads per MPI rank to start (0 is guess)
-ntomp_pme <int> (0)
Number of OpenMP threads per MPI rank to start (0 is -ntomp)
-pin <enum> (auto)
Whether mdrun should try to set thread affinities: auto, on, off
-pinoffset <int> (0)
The lowest logical core number to which mdrun should pin the first thread
-pinstride <int> (0)
Pinning distance in logical cores for threads, use 0 to minimize the number of threads per
physical core
-gpu_id <string>
List of GPU device id-s to use, specifies the per-node PP rank to GPU mapping
-[no]ddcheck (yes)
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, yes
-dds <real> (0.8)
Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in order to
provide a margin in which dynamic load balancing can act while preserving the minimum cell size.
-gcom <int> (-1)
Global communication frequency
-nb <enum> (auto)
Calculate non-bonded interactions on: auto, cpu, gpu, gpu_cpu
-nstlist <int> (0)
Set nstlist when using a Verlet buffer tolerance (0 is guess)
-[no]tunepme (yes)
Optimize PME load between PP/PME ranks or GPU/CPU
-[no]v (no)
Be loud and noisy
-[no]compact (yes)
Write a compact log file
-pforce <real> (-1)
Print all forces larger than this (kJ/mol nm)
-[no]reprod (no)
Try to avoid optimizations that affect binary reproducibility
-cpt <real> (15)
Checkpoint interval (minutes)
-[no]cpnum (no)
Keep and number checkpoint files
-[no]append (yes)
Append to previous output files when continuing from checkpoint instead of adding the simulation
part number to all file names
-nsteps <int> (-2)
Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option,
smaller is invalid)
-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 periodically with this period (steps)
-nex <int> (0)
Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero
or not specified gives neighbor replica exchange.
-reseed <int> (-1)
Seed for replica exchange, -1 is generate a seed
SEE ALSO
gmx(1) More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT
2015, GROMACS development team