----- Original Message ----- From: [email protected] Date: Wednesday, August 11, 2010 15:31 Subject: [gmx-users] dimer simulation To: [email protected]
> 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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