[gmx-users] Energy plots for specific atoms/selections

[Justin Lemkul]

On 2/6/20 4:35 AM, Bratin Kumar Das wrote:
> Hi
>      In this regard you have to follow the protein-ligand tutorial given by
> Dr lemkul. In mdp file you can mention the atoms of your interest and rerun
> the existing .xtc file...

The OP is not referring to the same case as an interaction energy; the 
approach is different (see my previous post on how to do this).

-Justin

> On Sat 1 Feb, 2020, 4:54 AM Daniel Burns, <dburns at iastate.edu> wrote:
>
>> Hi,
>>
>> I want to get an xvg file that will show me the LJ, Coulomb, and dihedral
>> energies on a specific set of atoms.  I've tried passing a .dat file with
>> the groups of atoms from gmx select to gmx enemat but I get an error
>> message saying that I must not have included those groups in my mdp file.
>> How do I incorporate them into my mdp file if I don't want specific mdp
>> options to work on them?
>>
>> I cannot figure out how to retrieve the data on my groups of interest. I've
>> tried -rerun and included an index of the atoms of interest as well
>>
>> If anybody has a detailed explanation, I would be grateful.
>>
>> Thank you,
>>
>> Dan
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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