Provided by: gromacs-openmpi_4.6.5-1build1_amd64 bug


       mdrun_mpi  -  performs  a  simulation, do a normal mode analysis or an energy minimization
       across multiple CPUs or systems

       VERSION 4.5


       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

       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

       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  -dhdl is only used when free energy calculation 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

       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, 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 system.

       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 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 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  -maxh*0.99 hours.

       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.
        Checkpoint file

       -cpo state.cpt Output, Opt.
        Checkpoint file

       -c confout.gro Output
        Structure file: gro g96 pdb etc.

       -e ener.edr Output
        Energy file

       -g md.log Output
        Log file

       -dhdl dhdl.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


        Print help info and quit

        Print version info and quit

       -nice int 0
        Set the nicelevel

       -deffnm string
        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

       -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 system



       More information about GROMACS is available at <>.

                                         Thu 26 Aug 2010                             mdrun_mpi(1)