[gmx-developers] Potential Energy Calculations from Topology
sanyam at nyu.edu
Mon Feb 5 22:12:31 CET 2018
Wow! I never got around to analysing the -rerun argument. Let me process
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:
> 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
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Masters in Computer Science
Courant Institute, New York University
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