A more complete answer is that to define energy groups for this reside and rest residues respectively, generate the tpr with grompp and then use mdrun -rerun to run through the existing trajectory to obtain what you wanted. Regards, Yang Ye
----- Original Message ---- From: Justin A. Lemkul <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Monday, September 1, 2008 5:37:47 AM Subject: Re: [gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein? Limei Zhang wrote: > Dear all, > > > > Is it possible to use GROMACS function(s) to calculate the averaged van > der Waals potential /Coulomb potential between a given residue and the > rest residues in the protein during a certain time of simulation? > > Different contributions to the potential can be analyzed by specifying the appropriate 'energygrps' in the .mdp file. -Justin > > Thanks, > > > > LZhang > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 -- ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
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