Commit 8a1e588a authored by Nicholas Breen's avatar Nicholas Breen

update mdrun_mpi.*.1

parent 610021fa
.\" Man page generated from reStructuredText.
.
.TH "MDRUN_MPI" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-MDRUN" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.SH NAME
mdrun_mpi \- Perform a simulation, do a normal mode analysis or an energy minimization
.
......@@ -55,9 +55,9 @@ mdrun_mpi [\fB\-s\fP \fI[<.tpr>]\fP] [\fB\-cpi\fP \fI[<.cpt>]\fP] [\fB\-table\fP
[\fB\-gputasks\fP \fI<string>\fP] [\fB\-[no]ddcheck\fP] [\fB\-rdd\fP \fI<real>\fP]
[\fB\-rcon\fP \fI<real>\fP] [\fB\-dlb\fP \fI<enum>\fP] [\fB\-dds\fP \fI<real>\fP] [\fB\-gcom\fP \fI<int>\fP]
[\fB\-nb\fP \fI<enum>\fP] [\fB\-nstlist\fP \fI<int>\fP] [\fB\-[no]tunepme\fP] [\fB\-pme\fP \fI<enum>\fP]
[\fB\-pmefft\fP \fI<enum>\fP] [\fB\-[no]v\fP] [\fB\-pforce\fP \fI<real>\fP] [\fB\-[no]reprod\fP]
[\fB\-cpt\fP \fI<real>\fP] [\fB\-[no]cpnum\fP] [\fB\-[no]append\fP] [\fB\-nsteps\fP \fI<int>\fP]
[\fB\-maxh\fP \fI<real>\fP] [\fB\-multi\fP \fI<int>\fP] [\fB\-replex\fP \fI<int>\fP] [\fB\-nex\fP \fI<int>\fP]
[\fB\-pmefft\fP \fI<enum>\fP] [\fB\-bonded\fP \fI<enum>\fP] [\fB\-[no]v\fP] [\fB\-pforce\fP \fI<real>\fP]
[\fB\-[no]reprod\fP] [\fB\-cpt\fP \fI<real>\fP] [\fB\-[no]cpnum\fP] [\fB\-[no]append\fP]
[\fB\-nsteps\fP \fI<int>\fP] [\fB\-maxh\fP \fI<real>\fP] [\fB\-replex\fP \fI<int>\fP] [\fB\-nex\fP \fI<int>\fP]
[\fB\-reseed\fP \fI<int>\fP]
.ft P
.fi
......@@ -124,7 +124,8 @@ For each different tabulated interaction type used, a table file name must
be given. For the topology to work, a file name given here must match a
character sequence before the file extension. That sequence is: an underscore,
then a ‘b’ for bonds, an ‘a’ for angles or a ‘d’ for dihedrals,
and finally the matching table number index used in the topology.
and finally the matching table number index used in the topology. Note that,
these options are deprecated, and in future will be available via grompp.
.sp
The options \fB\-px\fP and \fB\-pf\fP are used for writing pull COM
coordinates and forces when pulling is selected
......@@ -194,8 +195,10 @@ With option \fB\-maxh\fP a simulation is terminated and a checkpoint
file is written at the first neighbor search step where the run time
exceeds \fB\-maxh\fP*0.99 hours. This option is particularly useful in
combination with setting \fBnsteps\fP to \-1 either in the mdp or using the
similarly named command line option. This results in an infinite run,
terminated only when the time limit set by \fB\-maxh\fP is reached (if any)or upon receiving a signal.
similarly named command line option (although the latter is deprecated).
This results in an infinite run,
terminated only when the time limit set by \fB\-maxh\fP is reached (if any)
or upon receiving a signal.
.sp
When \fBmdrun\fP receives a TERM or INT signal (e.g. when ctrl+C is
pressed), it will stop at the next neighbor search step or at the
......@@ -411,6 +414,9 @@ Perform PME calculations on: auto, cpu, gpu
.B \fB\-pmefft\fP <enum> (auto)
Perform PME FFT calculations on: auto, cpu, gpu
.TP
.B \fB\-bonded\fP <enum> (auto)
Perform bonded calculations on: auto, cpu, gpu
.TP
.B \fB\-[no]v\fP (no)
Be loud and noisy
.TP
......@@ -435,9 +441,6 @@ Run this number of steps, overrides .mdp file option (\-1 means infinite, \-2 me
.B \fB\-maxh\fP <real> (\-1)
Terminate after 0.99 times this time (hours)
.TP
.B \fB\-multi\fP <int> (0)
Do multiple simulations in parallel
.TP
.B \fB\-replex\fP <int> (0)
Attempt replica exchange periodically with this period (steps)
.TP
......
.\" Man page generated from reStructuredText.
.
.TH "MDRUN_MPI" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-MDRUN" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.SH NAME
mdrun_mpi \- Perform a simulation, do a normal mode analysis or an energy minimization
.
......@@ -55,9 +55,9 @@ mdrun_mpi [\fB\-s\fP \fI[<.tpr>]\fP] [\fB\-cpi\fP \fI[<.cpt>]\fP] [\fB\-table\fP
[\fB\-gputasks\fP \fI<string>\fP] [\fB\-[no]ddcheck\fP] [\fB\-rdd\fP \fI<real>\fP]
[\fB\-rcon\fP \fI<real>\fP] [\fB\-dlb\fP \fI<enum>\fP] [\fB\-dds\fP \fI<real>\fP] [\fB\-gcom\fP \fI<int>\fP]
[\fB\-nb\fP \fI<enum>\fP] [\fB\-nstlist\fP \fI<int>\fP] [\fB\-[no]tunepme\fP] [\fB\-pme\fP \fI<enum>\fP]
[\fB\-pmefft\fP \fI<enum>\fP] [\fB\-[no]v\fP] [\fB\-pforce\fP \fI<real>\fP] [\fB\-[no]reprod\fP]
[\fB\-cpt\fP \fI<real>\fP] [\fB\-[no]cpnum\fP] [\fB\-[no]append\fP] [\fB\-nsteps\fP \fI<int>\fP]
[\fB\-maxh\fP \fI<real>\fP] [\fB\-multi\fP \fI<int>\fP] [\fB\-replex\fP \fI<int>\fP] [\fB\-nex\fP \fI<int>\fP]
[\fB\-pmefft\fP \fI<enum>\fP] [\fB\-bonded\fP \fI<enum>\fP] [\fB\-[no]v\fP] [\fB\-pforce\fP \fI<real>\fP]
[\fB\-[no]reprod\fP] [\fB\-cpt\fP \fI<real>\fP] [\fB\-[no]cpnum\fP] [\fB\-[no]append\fP]
[\fB\-nsteps\fP \fI<int>\fP] [\fB\-maxh\fP \fI<real>\fP] [\fB\-replex\fP \fI<int>\fP] [\fB\-nex\fP \fI<int>\fP]
[\fB\-reseed\fP \fI<int>\fP]
.ft P
.fi
......@@ -124,7 +124,8 @@ For each different tabulated interaction type used, a table file name must
be given. For the topology to work, a file name given here must match a
character sequence before the file extension. That sequence is: an underscore,
then a ‘b’ for bonds, an ‘a’ for angles or a ‘d’ for dihedrals,
and finally the matching table number index used in the topology.
and finally the matching table number index used in the topology. Note that,
these options are deprecated, and in future will be available via grompp.
.sp
The options \fB\-px\fP and \fB\-pf\fP are used for writing pull COM
coordinates and forces when pulling is selected
......@@ -194,8 +195,10 @@ With option \fB\-maxh\fP a simulation is terminated and a checkpoint
file is written at the first neighbor search step where the run time
exceeds \fB\-maxh\fP*0.99 hours. This option is particularly useful in
combination with setting \fBnsteps\fP to \-1 either in the mdp or using the
similarly named command line option. This results in an infinite run,
terminated only when the time limit set by \fB\-maxh\fP is reached (if any)or upon receiving a signal.
similarly named command line option (although the latter is deprecated).
This results in an infinite run,
terminated only when the time limit set by \fB\-maxh\fP is reached (if any)
or upon receiving a signal.
.sp
When \fBmdrun\fP receives a TERM or INT signal (e.g. when ctrl+C is
pressed), it will stop at the next neighbor search step or at the
......@@ -411,6 +414,9 @@ Perform PME calculations on: auto, cpu, gpu
.B \fB\-pmefft\fP <enum> (auto)
Perform PME FFT calculations on: auto, cpu, gpu
.TP
.B \fB\-bonded\fP <enum> (auto)
Perform bonded calculations on: auto, cpu, gpu
.TP
.B \fB\-[no]v\fP (no)
Be loud and noisy
.TP
......@@ -435,9 +441,6 @@ Run this number of steps, overrides .mdp file option (\-1 means infinite, \-2 me
.B \fB\-maxh\fP <real> (\-1)
Terminate after 0.99 times this time (hours)
.TP
.B \fB\-multi\fP <int> (0)
Do multiple simulations in parallel
.TP
.B \fB\-replex\fP <int> (0)
Attempt replica exchange periodically with this period (steps)
.TP
......
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