As usual, we must tell Gromacs what it will be doing using gmx grompp
before we can perform our production simulation. Since we want to start our run where we left off (after doing equilibration), we prepare the TPR input file based on the last frame of the position-restraints
with gmx grompp
:
cd ../MD
cp ../templates/md.mdp .
gmx grompp -f md.mdp -p ../top/4ake.top -c ../posres/posres.pdb -o md.tpr -maxwarn 3
The md.mdp
file uses different algorithms from the position-restraints
for the temperature and pressure coupling, which are known to reproduce the exact NPT ensemble distribution.
Run the simulation as usual with gmx mdrun
:
gmx mdrun -v -stepout 10 -s md.tpr -deffnm md -cpi
This will automatically utilize all available cores and GPUs if available. The -cpi
flag indicates that you want Gromacs to continue from a previous run. You can kill the job with CONTROL-C
, look at the output, then continue with exactly the same command line :
gmx mdrun -v -stepout 10 -s md.tpr -deffnm md -cpi
(Try it out!). The -cpi
flag can be used on the first run without harm. For a continuation to occur, Gromacs needs to find the checkpoint file md.cpt
and all output files (md.xtc
, md.edr
, md.log
) in the current directory.