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 <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
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 <[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
-- gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface
or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
