I have done 10ns Simulation of complex(Protein ligand) by gromacs tutorial command but for further extend for 200ns. I did by tutorial and confusion please guide?
Thankyou in Advance.
Run the simulation using the last checkpoint file i.e., md_10.cpt in same directory.
You can try following commands for 200ns:
gmx mdrun md_10 -cpi md_10.cpt -nsteps 100000000 -apend #(no. of nsteps required to reach 200ns time scale)
You can use the commands in a sequential manner,
$ gmx convert-tpr -s md_10.tpr -extend 190000 (time for further simulation in ps) -o md_200.tpr
$ gmx mdrun -s md_200.tpr -cpi state.cpt -noappend
It will start after the 10ns.
Further, you can concatenate all trajectories together.
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