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

[Daniel Burns]

Thanks, Justin.

I wanted to confirm that the plumed scaled topology function is working
properly on the selected atoms but maybe this isn't the right way.  I've
already confirmed that the system's total energy is different between a
scaled and unscaled system but the tutorial makes it sounds as if you can
expect a precise value based on your scaling factor if you plot the
energies for just the scaled atoms.

Thanks again!

Dan

On Wed, Feb 5, 2020 at 6:10 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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