Try to maximize the intra- and inter-peptide hydrophobic interactions? I guess it can share the same parameters, just guess, no much idea.
lina ________________________________________ From: [email protected] [[email protected]] on behalf of Vitaly Chaban [[email protected]] Sent: Wednesday, August 11, 2010 1:37 PM To: [email protected] Subject: [gmx-users] Re: dimer simulation I think your choice should depend on what bonds you expect between the two monomers forming a dimer. -- Dr. Vitaly Chaban > 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. > -- > Regards > Sanjay Kumar Upadhyay > Research Scholor > Protein Dynamics lab > Dept of Chemistry > IIT Powai, Mumbai, 400076 -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
