OPTIONS
Options to specify input files:
-s [<.tpr>] (topol.tpr)
Portable xdr run input file
-cpi [<.cpt>] (state.cpt) (Opt.)
Checkpoint file
-table [<.xvg>] (table.xvg) (Opt.)
xvgr/xmgr file
-tablep [<.xvg>] (tablep.xvg) (Opt.)
xvgr/xmgr file
-tableb [<.xvg> [...]] (table.xvg) (Opt.)
xvgr/xmgr file
-rerun [<.xtc/.trr/...>] (rerun.xtc) (Opt.)
Trajectory: xtc trr cpt gro g96 pdb tng
-ei [<.edi>] (sam.edi) (Opt.)
ED sampling input
-multidir [<dir> [...]] (rundir) (Opt.)
Run directory
-awh [<.xvg>] (awhinit.xvg) (Opt.)
xvgr/xmgr file
-membed [<.dat>] (membed.dat) (Opt.)
Generic data file
-mp [<.top>] (membed.top) (Opt.)
Topology file
-mn [<.ndx>] (membed.ndx) (Opt.)
Index file
Options to specify output files:
-o [<.trr/.cpt/...>] (traj.trr)
Full precision trajectory: trr cpt tng
-x [<.xtc/.tng>] (traj_comp.xtc) (Opt.)
Compressed trajectory (tng format or portable xdr format)
-cpo [<.cpt>] (state.cpt) (Opt.)
Checkpoint file
-c [<.gro/.g96/...>] (confout.gro)
Structure file: gro g96 pdb brk ent esp
-e [<.edr>] (ener.edr)
Energy file
-g [<.log>] (md.log)
Log file
-dhdl [<.xvg>] (dhdl.xvg) (Opt.)
xvgr/xmgr file
-field [<.xvg>] (field.xvg) (Opt.)
xvgr/xmgr file
-tpi [<.xvg>] (tpi.xvg) (Opt.)
xvgr/xmgr file
-tpid [<.xvg>] (tpidist.xvg) (Opt.)
xvgr/xmgr file
-eo [<.xvg>] (edsam.xvg) (Opt.)
xvgr/xmgr file
-px [<.xvg>] (pullx.xvg) (Opt.)
xvgr/xmgr file
-pf [<.xvg>] (pullf.xvg) (Opt.)
xvgr/xmgr file
-ro [<.xvg>] (rotation.xvg) (Opt.)
xvgr/xmgr file
-ra [<.log>] (rotangles.log) (Opt.)
Log file
-rs [<.log>] (rotslabs.log) (Opt.)
Log file
-rt [<.log>] (rottorque.log) (Opt.)
Log file
-mtx [<.mtx>] (nm.mtx) (Opt.)
Hessian matrix
-if [<.xvg>] (imdforces.xvg) (Opt.)
xvgr/xmgr file
-swap [<.xvg>] (swapions.xvg) (Opt.)
xvgr/xmgr file
Other options:
-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 ranks 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)
Whether mdrun should try to set thread affinities: auto, on, off
-pinoffset <int> (0)
The lowest logical core number to which mdrun should pin the first
thread
-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 unique GPU device IDs available to use
-gputasks <string>
List of GPU device IDs, mapping each PP task on each node to a
device
-[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.
-nb <enum> (auto)
Calculate non-bonded interactions on: auto, cpu, gpu
-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
-pme <enum> (auto)
Perform PME calculations on: auto, cpu, gpu
-pmefft <enum> (auto)
Perform PME FFT calculations on: auto, cpu, gpu
-bonded <enum> (auto)
Perform bonded calculations on: auto, cpu, gpu
-update <enum> (auto)
Perform update and constraints on: auto, cpu, gpu
-[no]v (no)
Be loud and noisy
-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 (-1 means infinite, -2 means use mdp
option, smaller is invalid)
-maxh <real> (-1)
Terminate after 0.99 times this time (hours)
-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 |