GROMACS version:2023
GROMACS modification: Yes
Plumed 2-2.9.0
I have run a metadynamics simulation for my protein complex for 100 ns and generated the free energy surface (FES). I want to extend the simulation for another 100 ns.
The output files I have are: COLVAR, confout.gro, ener.edr, HILLS, md.log, state.cpt and traj_comp.xtc.
Would really appreciate the guidance on how to proceed with extending/append the simulation?
Dear @gurpreet
This is a PLUMED more than a GROMACS question, as you have patched GROMACS and are using external functionalities.
In general, to continue a simulation, you have to provide the checkpoint (.cpt) file to mdrun with the flag -cpi. Since you want to continue the simulation with also PLUMED, you will have to pass again the flag and corresponding file, something like -plumed plumed.dat. This last file is the one where you defined what PLUMED is supposed to be doing and it is where you have to specify the keywords to restart the simulations. Take a look at their manual, here if you are doing metadynamics. There is going to be the keyword RESTART that has to be put somewhere plus some files to point to, probably.
Overall, the command will look like this more or less
gmx mdrun [...] -s prod.tpr -cpi prod.cpt -plumed plumed.dat
where the plumed.dat file is the updated one for the restart. I highly suggest you to backup the directory with the run files so that if the restart fails you do not modify/corrupt the outcome of the previous run!