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       mdrun  -  performs a simulation, do a normal mode analysis or an energy

       VERSION 4.0.1


       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


       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 (

       The option  -dgdl is only used when free energy perturbation 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, 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.


       -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


        Print help info and quit

       -nice int 19
        Set the nicelevel

       -deffnm string
        Set the default filename for all file options

        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

        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

        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

        Sum the energies at every step

        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)

        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

        Do glass simulation with special long range corrections

        Do  a  simulation including the effect of an X-Ray bombardment on your



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                                Thu 16 Oct 2008                       mdrun(1)