[gmx-developers] Potential Energy Calculations from Topology

[Sanyam Kapoor]

Wow! I never got around to analysing the -rerun argument. Let me process
this one.
Thank you!

On Mon, Feb 5, 2018 at 3:19 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/5/18 3:15 PM, Sanyam Kapoor wrote:
>
> Hello everyone,
>
> I've been trying to familiarize myself with the Gromacs codebase over the
> past couple weeks and have figured out various control flows.
>
> My question is in reference to the energy minimization step via "do_steep",
> which calls "evaluate_energy". Am I correct in understanding that this is
> the only function which calculates the potential energy of a topology
> state? It appears that this function is very tightly coupled with the
> multi-threading system and hence the concern.
>
> My aim is to build a C wrapper around this function but that will only be
> possible if I can get a bare bones energy estimator from the topology.
>
> Apologies for any technically incorrect statement, I don't actually have a
> Molecular Dynamics background.
>
>
> You should not invoke the energy minimizer at all. The process you want to
> carry out is best done with mdrun -rerun and a .tpr file that specifies
> zero MD steps:
>
> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> or send a mail to gmx-developers-request at gromacs.org.

-- 
Regards,
Sanyam Kapoor
Masters in Computer Science
Courant Institute, New York University
https://www.sanyamkapoor.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20180205/35d72ea7/attachment.html>