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以下是gmx_mpi mdrun -h的部分输出：
OPTIONS
Options to specify input and output files:
-s [<.tpr/.tpb/...>] (topol.tpr) (Input) Run input file: tpr tpb tpa
-o [<.trr/.cpt/...>] (traj.trr) (Output)
Full precision trajectory: trr cpt trj tng
-x [<.xtc/.tng>] (traj_comp.xtc) (Output, Opt.)
Compressed trajectory (tng format or portable xdr format)
-cpi [<.cpt>] (state.cpt) (Input, Opt.) Checkpoint file
-cpo [<.cpt>] (state.cpt) (Output, Opt.) Checkpoint file
-c [<.gro/.g96/...>] (confout.gro) (Output)
Structure file: gro g96 pdb brk ent esp
-e [<.edr>] (ener.edr) (Output) Energy file
-g [<.log>] (md.log) (Output) Log file
-dhdl [<.xvg>] (dhdl.xvg) (Output, Opt.) xvgr/xmgr file
-field [<.xvg>] (field.xvg) (Output, Opt.) xvgr/xmgr file
-table [<.xvg>] (table.xvg) (Input, Opt.) xvgr/xmgr file
-tabletf [<.xvg>] (tabletf.xvg) (Input, Opt.) xvgr/xmgr file
-tablep [<.xvg>] (tablep.xvg) (Input, Opt.) xvgr/xmgr file
-tableb [<.xvg>] (table.xvg) (Input, Opt.) xvgr/xmgr file
-rerun [<.xtc/.trr/...>] (rerun.xtc) (Input, Opt.)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-tpi [<.xvg>] (tpi.xvg) (Output, Opt.) xvgr/xmgr file
-tpid [<.xvg>] (tpidist.xvg) (Output, Opt.) xvgr/xmgr file
-ei [<.edi>] (sam.edi) (Input, Opt.) ED sampling input
-eo [<.xvg>] (edsam.xvg) (Output, Opt.) xvgr/xmgr file
-devout [<.xvg>] (deviatie.xvg) (Output, Opt.) xvgr/xmgr file
-runav [<.xvg>] (runaver.xvg) (Output, Opt.) xvgr/xmgr file
-px [<.xvg>] (pullx.xvg) (Output, Opt.) xvgr/xmgr file
-pf [<.xvg>] (pullf.xvg) (Output, Opt.) xvgr/xmgr file
-ro [<.xvg>] (rotation.xvg) (Output, Opt.) xvgr/xmgr file
-ra [<.log>] (rotangles.log) (Output, Opt.) Log file
-rs [<.log>] (rotslabs.log) (Output, Opt.) Log file
-rt [<.log>] (rottorque.log) (Output, Opt.) Log file
-mtx [<.mtx>] (nm.mtx) (Output, Opt.) Hessian matrix
-dn [<.ndx>] (dipole.ndx) (Output, Opt.) Index file
-multidir [<dir> [...]] (rundir) (Input, Opt.) Run directory
-membed [<.dat>] (membed.dat) (Input, Opt.) Generic data file
-mp [<.top>] (membed.top) (Input, Opt.) Topology file
-mn [<.ndx>] (membed.ndx) (Input, Opt.) Index file
-if [<.xvg>] (imdforces.xvg) (Output, Opt.) xvgr/xmgr file
-swap [<.xvg>] (swapions.xvg) (Output, Opt.) xvgr/xmgr file
Other options:
-nice <int> (0) Set the nicelevel
-deffnm <string> Set the default filename for all file options
-xvg <enum> (xmgrace) xvg plot formatting: xmgrace, xmgr, none
-dd <vector> (0 0 0) Domain decomposition grid, 0 is optimize
-ddorder <enum> (interleave) DD rank order: interleave, pp_pme, cartesian
-npme <int> (-1)
Number of separate ranks 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 rank to start (0 is guess)
-ntomp_pme <int> (0)
Number of OpenMP threads per MPI rank to start (0 is -ntomp)
-pin <enum> (auto) Set thread affinities: auto, on, 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]ddcheck (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, yes
-dds <real> (0.8)
Fraction in (0,1) by whose reciprocal the initial DD cell size will be
increased in order to provide a margin in which dynamic load balancing
can act while preserving the minimum cell size.
-gcom <int> (-1) Global communication frequency
-nb <enum> (auto)
Calculate non-bonded interactions on: auto, cpu, gpu, gpu_cpu
-nstlist <int> (0)
Set nstlist when using a Verlet buffer tolerance (0 is guess)
-[no]tunepme (yes) Optimize PME load between PP/PME ranks or GPU/CPU
-[no]testverlet (no) Test the Verlet non-bonded scheme
-[no]v (no) Be loud and noisy
-[no]compact (yes) Write a compact log file
-[no]seppot (no)
Write separate V and dVdl terms for each interaction type and rank to the
log file(s)
-pforce <real> (-1) Print all forces larger than this (kJ/mol nm)
-[no]reprod (no)
Try to avoid optimizations that affect binary reproducibility
-cpt <real> (15) Checkpoint interval (minutes)
-[no]cpnum (no) Keep and number checkpoint files
-[no]append (yes)
Append to previous output files when continuing from checkpoint instead
of adding the simulation part number to all file names
-nsteps <int> (-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
加 -gpu_id参数，显卡的编号从0开始 |
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发表于 Post on 2018-4-4 15:04:38
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发表于 Post on 2018-5-31 17:43:29
