Provided by: gromacs-data_4.6.5-1build1_all 
NAME
mdrun - performs a simulation, do a normal mode analysis or an energy minimization
VERSION 4.6.5
SYNOPSIS
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 -dhdl dhdl.xvg -field field.xvg -table table.xvg -tabletf tabletf.xvg
-tablep tablep.xvg -tableb table.xvg -rerun rerun.xtc -tpi tpi.xvg -tpid tpidist.xvg -ei
sam.edi -eo edsam.xvg -j wham.gct -jo bam.gct -ffout gct.xvg -devout deviatie.xvg -runav
runaver.xvg -px pullx.xvg -pf pullf.xvg -ro rotation.xvg -ra rotangles.log -rs
rotslabs.log -rt rottorque.log -mtx nm.mtx -dn dipole.ndx -multidir rundir -membed
membed.dat -mp membed.top -mn membed.ndx -[no]h -[no]version -nice int -deffnm string -xvg
enum -[no]pd -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 -[no]tunepme -[no]testverlet -[no]v
-[no]compact -[no]seppot -pforce real -[no]reprod -cpt real -[no]cpnum -[no]append -nsteps
step -maxh real -multi int -replex int -nex int -reseed int -[no]ionize
DESCRIPTION
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, unless set on the command line, the number of MPI threads will automatically
be set to the number of GPUs detected. To use a subset of the available GPUs, or to
manually provide a mapping of GPUs to PP ranks, you can use the -gpu_id option. The
argument of -gpu_id is a string of digits (without delimiter) representing device id-s of
the GPUs to be used. For example, " 02" specifies using GPUs 0 and 2 in the first and
second PP ranks per compute node respectively. To select different sets of GPU-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, with the difference that an
environment variable can have different values on different compute nodes. Multiple MPI
ranks on each node can share GPUs. This is accomplished by specifying the id(s) of the
GPU(s) multiple times, e.g. " 0011" for four ranks sharing two GPUs in this node. This
works within a single simulation, or a multi-simulation, with any form of MPI.
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.
FILES
-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
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
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]pdno
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 device id-s to use, specifies the per-node PP rank to GPU mapping
-[no]ddcheckyes
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]tunepmeyes
Optimize PME load between PP/PME nodes or GPU/CPU
-[no]testverletno
Test the Verlet non-bonded scheme
-[no]vno
Be loud and noisy
-[no]compactyes
Write a compact log file
-[no]seppotno
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]reprodno
Try to avoid optimizations that affect binary reproducibility
-cpt real 15
Checkpoint interval (minutes)
-[no]cpnumno
Keep and number checkpoint files
-[no]appendyes
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 (N3 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]ionizeno
Do a simulation including the effect of an X-Ray bombardment on your system
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 2 Dec 2013 mdrun(1)