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--- howto:bioinformatics:gromacs [2013/11/22 12:05]
dane [Gromacs help]
+++ — (current)
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-====== Running Gromacs ======
-===== Before you start =====
-Before running your scripts remember to run((Note: Make sure the line:<code bash>export MODULEPATH=/opt/gridware/bioinformatics/modules:$MODULEPATH</code>exists in your //~/.profile// file)):<code bash>user@login01:~ $ module add gromacs/4.6.3</code>
-===== Job script =====
-Then your job script called //my_job.msub// will look something like this:
-<file bash my_job.msub>
-#/bin/sh
-#MSUB -l procs=64
-#MSUB -l feature=dell
-#MSUB -l walltime=10:00:00
-#MSUB -m be
-#MSUB -V
-#MSUB -o ${HOME}/scratch5/GROMACS/stdout.txt
-#MSUB -e ${HOME}/scratch5/GROMACS/stderr.txt
-#MSUB -d ${HOME}/scratch5/GROMACS/
-#MSUB -N MyGromacsJob
-#MSUB -mb
-NP=`cat ${PBS_NODEFILE} | wc -l`
-EXE=mdrun
-ARGS="-s input.tpr -deffnm input.tpr"
-mpirun -np ${NP} -machinefile ${PBS_NODEFILE} ${EXE} ${ARGS}
-</file>
-===== Submit your job =====
-Finally submit your job using:<code bash>user@login01:~ $ msub my_job.msub</code>
-===== Gromacs help =====
-obtained by running:<code bash>user@login01:~ $ mdrun -h</code>
-----------
-<code>
-                         :-)  G  R  O  M  A  C  S  (-:
-               Giant Rising Ordinary Mutants for A Clerical Setup
-                            :-)  VERSION 4.6.3  (-:
-        Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
-           Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
-     Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
-        Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
-           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
-                Michael Shirts, Alfons Sijbers, Peter Tieleman,
-               Berk Hess, David van der Spoel, and Erik Lindahl.
-       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
-         Copyright (c) 2001-2012,2013, The GROMACS development team at
-        Uppsala University & The Royal Institute of Technology, Sweden.
-            check out http://www.gromacs.org for more information.
-         This program is free software; you can redistribute it and/or
-       modify it under the terms of the GNU Lesser General Public License
-        as published by the Free Software Foundation; either version 2.1
-             of the License, or (at your option) any later version.
-                                :-)  mdrun  (-:
-</code>
-==== Description ====
-<code>
------------
-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 -dhdl is only used when free energy calculation is turned on.
-A simulation can be run in parallel using two different parallelization
-schemes: MPI parallelization and/or OpenMP thread parallelization. The MPI
-parallelization uses multiple processes when mdrun is compiled with a normal
-MPI library or threads when mdrun is compiled with the GROMACS built-in
-thread-MPI library. OpenMP threads are supported when mdrun is compiled with
-OpenMP. Full OpenMP support is only available with the Verlet cut-off scheme,
-with the (older) group scheme only PME-only processes can use OpenMP
-parallelization. In all cases mdrun will by default try to use all the
-available hardware resources. With a normal MPI library only the options
--ntomp (with the Verlet cut-off scheme) and -ntomp_pme, for PME-only
-processes, can be used to control the number of threads. With thread-MPI
-there are additional options -nt, which sets the total number of threads, and
--ntmpi, which sets the number of thread-MPI threads. Note that using combined
-MPI+OpenMP parallelization is almost always slower than single
-parallelization, except at the scaling limit, where especially OpenMP
-parallelization of PME reduces the communication cost. OpenMP-only
-parallelization is much faster than MPI-only parallelization on a single
-CPU(-die). Since we currently don't have proper hardware topology detection,
-mdrun compiled with thread-MPI will only automatically use OpenMP-only
-parallelization when you use up to 4 threads, up to 12 threads with Intel
-Nehalem/Westmere, or up to 16 threads with Intel Sandy Bridge or newer CPUs.
-Otherwise MPI-only parallelization is used (except with GPUs, see below).
-To quickly test the performance of the new Verlet cut-off scheme with old
-.tpr files, either on CPUs or CPUs+GPUs, you can use the -testverlet option.
-This should not be used for production, since it can slightly modify
-potentials and it will remove charge groups making analysis difficult, as the
-.tpr file will still contain charge groups. For production simulations it is
-highly recommended to specify cutoff-scheme = Verlet in the .mdp file.
-With GPUs (only supported with the Verlet cut-off scheme), the number of GPUs
-should match the number of MPI processes or MPI threads, excluding PME-only
-processes/threads. With thread-MPI the number of MPI threads will
-automatically be set to the number of GPUs detected. When you want to use a
-subset of the available GPUs, you can use the -gpu_id option, where GPU id's
-are passed as a string, e.g. 02 for using GPUs 0 and 2. When you want
-different GPU id's on different nodes of a compute cluster, use the
-GMX_GPU_ID environment variable instead. The format for GMX_GPU_ID is
-identical to -gpu_id, but an environment variable can have different values
-on different nodes of a cluster.
-When using PME with separate PME nodes or with a GPU, the two major compute
-tasks, the non-bonded force calculation and the PME calculation run on
-different compute resources. If this load is not balanced, some of the
-resources will be idle part of time. With the Verlet cut-off scheme this load
-is automatically balanced when the PME load is too high (but not when it is
-too low). This is done by scaling the Coulomb cut-off and PME grid spacing by
-the same amount. In the first few hundred steps different settings are tried
-and the fastest is chosen for the rest of the simulation. This does not
-affect the accuracy of the results, but it does affect the decomposition of
-the Coulomb energy into particle and mesh contributions. The auto-tuning can
-be turned off with the option -notunepme.
-mdrun pins (sets affinity of) threads to specific cores, when all (logical)
-cores on a compute node are used by mdrun, even when no multi-threading is
-used, as this usually results in significantly better performance. If the
-queuing systems or the OpenMP library pinned threads, we honor this and don't
-pin again, even though the layout may be sub-optimal. If you want to have
-mdrun override an already set thread affinity or pin threads when using less
-cores, use -pin on. With SMT (simultaneous multithreading), e.g. Intel
-Hyper-Threading, there are multiple logical cores per physical core. The
-option -pinstride sets the stride in logical cores for pinning consecutive
-threads. Without SMT, 1 is usually the best choice. With Intel
-Hyper-Threading 2 is best when using half or less of the logical cores, 1
-otherwise. The default value of 0 do exactly that: it minimizes the threads
-per logical core, to optimize performance. If you want to run multiple mdrun
-jobs on the same physical node,you should set -pinstride to 1 when using all
-logical cores. When running multiple mdrun (or other) simulations on the same
-physical node, some simulations need to start pinning from a non-zero core to
-avoid overloading cores; with -pinoffset you can specify the offset in
-logical cores for pinning.
-When mdrun is started using MPI with more than 1 process or with thread-MPI
-with more than 1 thread, MPI 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, 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 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.
-With -multi or -multidir, multiple systems can be simulated in parallel. As
-many input files/directories are required as the number of systems. The
--multidir option takes a list of directories (one for each system) and runs
-in each of them, using the input/output file names, such as specified by e.g.
-the -s option, relative to these directories. With -multi, 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 or -multidir option, described
-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 -membed does what used to be g_membed, i.e. embed a protein into a
-membrane. The data file should contain the options that where passed to
-g_membed before. The -mn and -mp both apply to this as well.
-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.
-</code>
-==== Options ====
-<code>
-Option     Filename  Type         Description
-------------------------------------------------------------
-  -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
--tabletf    tabletf.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      edsam.xvg  Output, Opt. xvgr/xmgr file
-  -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
- -ro   rotation.xvg  Output, Opt. xvgr/xmgr file
- -ra  rotangles.log  Output, Opt. Log file
- -rs   rotslabs.log  Output, Opt. Log file
- -rt  rottorque.log  Output, Opt. Log file
--mtx         nm.mtx  Output, Opt. Hessian matrix
- -dn     dipole.ndx  Output, Opt. Index file
--multidir    rundir  Input, Opt., Mult. Run directory
--membed  membed.dat  Input, Opt.  Generic data file
- -mp     membed.top  Input, Opt.  Topology file
- -mn     membed.ndx  Input, Opt.  Index file
-Option       Type   Value   Description
-------------------------------------------------------
--[no]h       bool   yes     Print help info and quit
--[no]version bool   no      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
--[no]pd      bool   no      Use particle decompostion
--dd          vector 0 0 0   Domain decomposition grid, 0 is optimize
--ddorder     enum   interleave  DD node order: interleave, pp_pme or cartesian
--npme        int    -1      Number of separate nodes 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 process/thread
-                            to start (0 is guess)
--ntomp_pme   int    0       Number of OpenMP threads per MPI process/thread
-                            to start (0 is -ntomp)
--pin         enum   auto    Fix threads (or processes) to specific cores:
-                            auto, on or off
--pinoffset   int    0       The starting logical core number for pinning to
-                            cores; used to avoid pinning threads from
-                            different mdrun instances to the same core
--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 id's to use
--[no]ddcheck bool   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 or yes
--dds         real   0.8     Minimum allowed dlb scaling of the DD cell size
--gcom        int    -1      Global communication frequency
--nb          enum   auto    Calculate non-bonded interactions on: auto, cpu,
-                            gpu or gpu_cpu
--[no]tunepme bool   yes     Optimize PME load between PP/PME nodes or GPU/CPU
--[no]testverlet bool   no      Test the Verlet non-bonded scheme
--[no]v       bool   no      Be loud and noisy
--[no]compact bool   yes     Write a compact log file
--[no]seppot  bool   no      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]reprod  bool   no      Try to avoid optimizations that affect binary
-                            reproducibility
--cpt         real   15      Checkpoint interval (minutes)
--[no]cpnum   bool   no      Keep and number checkpoint files
--[no]append  bool   yes     Append to previous output files when continuing
-                            from checkpoint instead of adding the simulation
-                            part number to all file names
--nsteps      step   -2      Run this number of steps, overrides .mdp file
-                            option
--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
--[no]ionize  bool   no      Do a simulation including the effect of an X-Ray
-                            bombardment on your system
-</code>

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