[gmx-users] g_lie and ligand only simulation

[Justin Lemkul]

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.
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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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