NVT simulation and mdp file

User discussions
1

GROMACS version: 2023
GROMACS modification: No

Hello,

I hope you’re doing well.

I have a question regarding the simulation of a 30-amino acid peptide in water. In the MDP file, would it be more appropriate to define tc-grps as system instead of Protein Non-Protein?

Also, I’ve come across papers suggesting that for NVT equilibration, a typical simulation time is 1 nanosecond. From what I understand, even for larger systems, equilibration times tend to range between 500 ps and 1 ns. I would appreciate the insights of anyone with experience—do you think 1 ns might be too long?

Lastly, if I use tc-grps = system, when defining define = -DPOSRES, will GROMACS still be able to recognize the peptide separately and apply restraints as needed?

2

With such a small peptide, the temperature should spread properly, so I would recommend tc-grps = system.

It is very difficult to say how long you need to equilibrate, for small systems you might manage with 0.5-1 ns. But large systems, inflexible systems and/or low temperature simulations, may require equilibration times in the 100-1000 ns range.

The POSRES definition (define = -DPOSRES) does not have anything to do with temperature coupling groups. It just activates sections in

#ifdef POSRES
...
#endif

in the topology file (or included itp files).

3

Thank you so much for your detailed response.
Your explanation really helped clarify things for me.