[gmx-users] GROMACS command for energy calculation

[Mark Abraham]

On 27/08/2012 8:32 PM, Acoot Brett wrote:
> 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?

I have no idea what you mean. Make the index groups in the index file 
and use them with commands like grompp -n yourindexfile.ndx -f 
yourparams.mdp

Mark

>
> 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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