5. Equilibrium molecular dynamics

5.1. Set up the production run

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-restrained equilibration 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-restrained equilibration for the temperature and pressure coupling, which are known to reproduce the exact NPT ensemble distribution.

5.2. Run the simulation

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.