general run commands

generate the binary run control file topol.tpr

mdout.mdp (record and explanation of the options)

gmx grompp -f xxx.mdp -c conf.gro -p field.top

run the molecular dynamics

the -v flag causes more info to be printed

many of the options indicated on the web don't seem to work??

manual

gmx mdrun -v

produces many files!

confout.gro (structure gromacs format of the last step)

ener.edr (binary energies,temp,pressure, box size, density etc)

mdout.mdp (run parameters)

md.log (log file)

traj.trrr (binary x,v and f)

traj_comp.xtc (compressed trajectory file)

state.cpt (current checkpoint file)

state_prev.cpt (previous checkpoint file)

undertaking a restart

less ideal is from a *.gro file, this has structure and velocities

best is from a checkpoint file *.cpt file as this retains high precision and thermal/pressure coupling

using the default checkpoint state.cpt file

data will be appended to existing log files force new files by -noappend

gmx mdrun -v -cpi state

making changes to to *.mdp file

very likely as you will need to extend the number of steps!

gmx grompp -f changed.mdp -c confout.gro -p field.top -o topol_new.tpr
gmx mdrun -s topol_new.tpr -cpi state.cpt

to run on cx1

generate the *.tpr file

copy over the needed base files

don't forget you need to load the application first

module load gromacs/2018.2 mpi intel-suite

run grompp on cx1 (this will give you a 2018.2 *.tpr file)

then execute for mdrun

you will need a run script

copy the following into a run-script called "rngmx"

where -nt is the total number of threads to start

and -v asks to print verbose information to screen

edit for the correct number of processors!

submit the script with the following command

qsub -N job_name rngmx

submit script

#!/bin/sh

# submit jobs to the que with this script using the following command:
# qsub -N name rngmx

# batch processing commands
#PBS -l walltime=72:00:00
#PBS -lselect=1:ncpus=24:mem=90000MB
#PBS -j oe
#PBS -q pqph

# load modules
#
  module load gromacs/2018.2 mpi intel-suite

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directoiry from which the job was sumbited.
   echo "tmpdir $TMPDIR"
   echo "cp $PBS_O_WORKDIR/field.top"
   cp $PBS_O_WORKDIR/field.top $TMPDIR/.
   echo "cp $PBS_O_WORKDIR/nvt_prep.mdp"
   cp $PBS_O_WORKDIR/nvt_prep.mdp $TMPDIR/.
   echo "cp $PBS_O_WORKDIR/topol.tpr"
   cp $PBS_O_WORKDIR/topol.tpr $TMPDIR/.
#
# run gromacs
#
  pbsexec gmx mdrun -nt 24 -v

  cp $TMPDIR/confout.gro $PBS_O_WORKDIR/.
  cp $TMPDIR/ener.edr $PBS_O_WORKDIR/.
  cp $TMPDIR/mdout.mdp $PBS_O_WORKDIR/.
  cp $TMPDIR/ener.edr $PBS_O_WORKDIR/.
  cp $TMPDIR/mdout.mdp $PBS_O_WORKDIR/.
  cp $TMPDIR/md.log $PBS_O_WORKDIR/.
  cp $TMPDIR/traj.trrr $PBS_O_WORKDIR/.
  cp $TMPDIR/traj_comp.xtc $PBS_O_WORKDIR/.
  cp $TMPDIR/state.cpt $PBS_O_WORKDIR/.
# exit