Hello folks,
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
Normally, the restraints should be gradually released during the equilibration MD simulation; the final part of the equilibration MD simulation should be performed without any restraints and the simulation parameters should be identical to those subsequently applied in the production MD simulation.
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The restraining will likely have the greatest effect on the least stable complex, thus obfuscating the goal of exploring the stability of the protein-ligand complexes.
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If your system is non-periodic, e.g., a sphere, and the entire system is within the sphere then applying a positional restraint is necessary, but it should be sufficient to restrain just one atom (of the protein) located close to the center of the sphere. If a part of the protein extends beyond the boundary of the sphere, no positional restraint is necessary if the simulated part of the protein does not undergo large conformational changes during MD simulation.
While performing production run in molecular dynamics simulations, there is no need to restraint your system (as you wish to see the dynamic behavior of your system). Restraint helps in equilibration of your system.
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