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       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 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 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

       *  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 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)

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