[gmx-users] g_lie and ligand only simulation

[Kavyashree M]

Sir,

Thank you. Should the ligand-water MD be done without PME?

Thank you
Regards

Kavya


On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul <jalemkul at 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
>
> --
> ==================================================
>
> 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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