[gmx-users] Using the md integrator for calculating free energy of solvation
jalemkul at vt.edu
Mon Apr 3 20:05:27 CEST 2017
On 4/3/17 2:01 PM, Dan Gil wrote:
> 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.
People have already done such a comparison and that's why grompp is telling you
this - it's better to use the Langevin integrator. You'll get better sampling,
particularly towards the end states. Using -maxwarn tells grompp "you're trying
to prevent me from making a mistake, but I want to do it anyway" :) You'd
better have a really, really good reason to try to override it.
> Best Regards,
> 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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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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