----- Original Message ----- From: sanja...@iitb.ac.in Date: Wednesday, August 11, 2010 15:31 Subject: [gmx-users] dimer simulation To: gmx-users@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
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
