Using restraints in production MD for Protein-Ligand complex

User discussions
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1

GROMACS version: 2020.5
GROMACS modification: Yes

Hi
I am trying to run a simulation for protein-ligand complex according to the Protein-Ligand complex tutorial on www.mdtutorials.com. While running the final Production MD I got the following error:

Screenshot from 2021-09-17 10-59-34
Screenshot from 2021-09-17 10-59-341848×1173 239 KB

As far as I understood here we need to provide a .gro file for position restraints. So I provided the npt.gro file with -r option using the following command:

gmx_mpi grompp -f md.mdp -c npt.gro -r npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_500.tpr

after this I got this warning:

Screenshot from 2021-09-17 11-15-05
Screenshot from 2021-09-17 11-15-051848×1173 210 KB

I used -maxwarn 1 option and was able to run the simulation properly.
However, in literature it is mentioned that restraints are only mentioned upto equilibriation step since for studying dynamics all molecules should be free for motion. If this is right then how can I overcome this error without using -r option and why is GROMACS showing this error?

Regards
Nupur

2

There should be no restraints in the production phase of the tutorial. If you’re doing something else or making modifications to the provided files, you will have to provide more detail about what you’re doing.