I am considering running an MD simulation of a protein with varying ligand concentrations. I think replica exchange molecular dynamics should be able to do that, but I have no idea how that is done.
Is it possible to get a tutorial or possibly other methods for running such a simulation?
Hello,
If in each of the replicas, you have different particle numbers (# of ligands) and you plan to use that variable as an exchange variable in the replica exchange algorithm, then I think it would not work in the ensemble that usually people use in MD (NPT).
You have to simulate your system in the grand canonical ensemble (uPT) and control the exchange probability of your ligands with the ligand reservoir to keep your chemical potential fixed.
I think this is not so simple and I don't remember a package that simulates such an ensemble in a simple/direct way.
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