[gmx-users] Using the md integrator for calculating free energy of solvation

Justin Lemkul jalemkul at vt.edu
Mon Mar 27 18:51:55 CEST 2017

On 3/26/17 9:40 PM, Dan Gil wrote:
> Hi,
> I am following Dr. Sander Pronk's and Dr. Justin Lemkul's tutorial on
> calculating free energy of solvation. Is it possible and theoretically
> sound to use the md integrator instead of the sd integrator for these
> calculations?

Langevin dynamics gives better sampling so it is frequently used for free energy 
calculations.  You may get comparable results with the leap-frog integrator, but 
I haven never done a side-by-side comparison.


> I have already done a considerable amount of work using md integration, and
> I want to make sure that the free energy values I calculate are consistent
> with my previous work.
> If using the md integrator is not sound, is there an alternative way of
> calculating solvation energy that will be consistent?
> Best Regards,
> Dan


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


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