[gmx-users] GROMACS command for energy calculation
acootbrett at yahoo.com
Mon Aug 27 11:42:33 CEST 2012
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?
----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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