[gmx-users] dimer simulation
mark.abraham at anu.edu.au
Wed Aug 11 10:08:13 CEST 2010
----- 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.
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