[gmx-users] Re: dimer simulation

#ZHAO LINA# ZHAO0139 at e.ntu.edu.sg
Wed Aug 11 07:57:44 CEST 2010

Try to maximize the intra- and inter-peptide hydrophobic interactions?
I guess it can share the same parameters, just guess, no much idea. 

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Vitaly Chaban [vvchaban at gmail.com]
Sent: Wednesday, August 11, 2010 1:37 PM
To: gmx-users at gromacs.org
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
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