[gmx-users] GROMACS command for energy calculation

[Mark Abraham]

On 27/08/2012 7:42 PM, Acoot Brett wrote:
> 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?

An index file *contains* definitions of index groups. You need an index 
file that defines every group you care about, and you refer to the names 
of those groups in your .mdp file.

Mark

>   
> 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
>