[gmx-users] dimer simulation

[Mark Abraham]

----- Original Message -----
From: sanjay23 at iitb.ac.in
Date: Wednesday, August 11, 2010 15:31
Subject: [gmx-users] dimer simulation
To: gmx-users at gromacs.org

> Dear gmx-users
> I want to simulate a protein which biological function defined 
> by dimer
> formation. I need to simulate this protein in dimer as well as in
> monomeric form to solve my objectives. I am using Gromacs-4.0.4 for
> simulation. I have a doubt, is there any specific parameters for dimer
> simulation or we have to use similar parameters like monomer protein
> simulation. I read some literature's on dimer simulation but 
> they are
> using similar parameters like monomer.

Making ad hoc changes to force fields just asks for trouble. Needing to ask whether you should make changes to force fields guarantees it :-) See http://www.gromacs.org/Documentation/Terminology/Force_Fields

There's nothing magic about protein dimerization by comparison with any other protein-protein intra- or inter-molecular interaction. The same model physics should cope with them all.

Mark

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