Dear Justin, For example, I want to calculate the energy between residue 50 and residue 100, then I create an index file (A), then in the MDP file I will insert energygryp=A (with indec file extension or not?), then do the rerun, am I right? Cheers, Acoot
----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Acoot Brett <acootbr...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Monday, 27 August 2012 9:53 AM Subject: Re: [gmx-users] GROMACS command for energy calculation On 8/26/12 7:44 PM, Acoot Brett wrote: > Dear All, > > I am still confused and I hope I can get some detailed explaination. For > example, I want to determine the interaction energy between residue 52 and > residue 105, how should I set energyggryp and what is the related commands? > > And if I want to determine the interaction energy between residue 52 in China > A and residue 8 in Chain B, what will be the difference? > > You can also tell me a internet link on it. > The help information from make_ndx is what you need. Type "help" at the prompt (without quotes) and you will see examples. For instance, to select residue 52 of chain A: ch A & r 52 That creates a group that you can then use as an energygrp in the .mdp file. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
