[gmx-users] GROMACS command for energy calculation

[Acoot Brett]

Hi Mark,
 
Then MAP file has the ability to recognize the groups saved in the index file, which is in the same folder as the MDP file? 

Acoot


----- Original Message -----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Monday, 27 August 2012 8:00 PM
Subject: Re: [gmx-users] GROMACS command for energy calculation

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
> 

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