On 11/2/13 12:14 PM, Kavyashree M wrote:
Sir,
Thank you. Should the ligand-water MD be done without PME?
I already answered this. Please read my previous reply again.
-Justin
Thank you
Regards
Kavya
On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/2/13 1:22 AM, Kavyashree M wrote:
Dear Users,
Its mentioned in the list that it would be
wrong to use g_lie on a simulation which
uses PME.
So kindly suggest any other way available
to get the free energy of ligand binding other
using g_lie?
The original simulation should be done with PME, then the energies
recalculated using mdrun -rerun without PME. More detailed methods are
available in the list archive; this topic gets discussed a lot.
-Justin
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Justin A. Lemkul, Ph.D.
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==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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