[gmx-users] g_lie and ligand only simulation

[Justin Lemkul]

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 <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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-- 
==================================================

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

==================================================