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

[Justin Lemkul]

On 1/31/20 6:23 PM, Daniel Burns 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.

Create an index file that defines the atoms of interest, create a 
matching trajectory with trjconv and new .tpr file with only those atoms 
using convert-tpr, then use mdrun -rerun with those new files. Be 
advised that simply chopping out atoms and computing energies like this 
is unlikely to have any physical meaning.

-Justin

-- 
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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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