[gmx-users] Protein and Ligand position restraint

[Amir Zeb]

Hello gmx users,

I want to conduct md simulation to explore the comparative stability and
interaction mechanism of the reference compound (experimentally determined)
and the newly screened candidate molecules by virtual screening approach.
The gromacs version 5.0.7 is installed on my cluster. I want to listen to
your suggestions regarding:

1. Is it rational to restraint the position of the protein and/or ligand?
2. If position restraint is necessary, which part of the system should I
restraint?
3. Also, at which steps, I may restraint them, means NVT, NPT and md
production? Because the Justin tutorial mentioned the release of restraint
immediately after equilibration steps.

I have co-factor FAD as the essential part of the protein, so I would like
to consider protein-FAD as single moiety. I searched from gmx-user archive
and Justin Tutorial, but I could not get a sound proof for this dilemma.

Hope to listen to you soon

Thanks

Amir