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 <[email protected]>
To: Acoot Brett <[email protected]>; Discussion list for GROMACS users
<[email protected]>
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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