[gmx-users] Using the md integrator for calculating free energy of solvation
dan.gil9973 at gmail.com
Mon Apr 3 20:01:19 CEST 2017
Thank you Dr. Lemkul,
I am trying to run grompp with the md integrator, but I am getting this
"For proper sampling of the (nearly) decoupled state, stochastic dynamics
should be used"
Should I ignore this warning with the -maxwarn option and try running it? I
will see if I obtain comparable values for ethanol.
On Mon, Mar 27, 2017 at 12:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 3/26/17 9:40 PM, Dan Gil wrote:
>> 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
> 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,
> 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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