[gmx-users] GROMACS command for energy calculation

[Acoot Brett]

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 <jalemkul at vt.edu>
To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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

-- 
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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

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