[gmx-developers] Potential Energy Calculations from Topology

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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