[gmx-users] Doubt about Free Energy control Minimization

[Justin Lemkul]

On 6/13/17 4:31 PM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> I aspire to derive energy-minimum structures when the interaction potential energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1.
> 
> I presume the following Free Energy minimization code mentioned in gromacs tutorial may do the trick. I would appreciate if you could please verify if it produces my intended result.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp
> 

Possibly, but the outcomes may be unphysical.

-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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