Perhaps your *.mdp files could be missing, there a total of 5 *.mdp files (em, em_real, md, npt, nvt). Also you need to do certain editing in several files like, topol.top and in some of these *.mdp files. Hope it helps, all the best.

gmx grompp -f md.mdp -c npt.gro -t npt.cpt -n index_protein_ligand.ndx -p topol.top -o md_200ns.tpr

gmx mdrun -v -deffnm md_200ns

These are the commands I used.

Your tpr file is named md_200ns.tpr

Try using the command

gmx mdrun -v -deffnm md_200ns

Good luck...

Perhaps your *.mdp files could be missing, there a total of 5 *.mdp files (em, em_real, md, npt, nvt). Also you need to do certain editing in several files like, topol.top and in some of these *.mdp files. Hope it helps, all the best.

Thank you all for your answers. I was running the NVT, NPT and MD in a cluster which has gromacs 4.6 installed.

I generated the initial files til energy minimization in my computer, which has 5.1.4 installed.

The problem arised because of difference in versions. I installed 4.6 on my computer and all is good now.