[gmx-developers] Potential Energy Calculations from Topology

Justin Lemkul jalemkul at vt.edu
Mon Feb 5 21:19:01 CET 2018

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) 231-3129


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