[gmx-users] g_lie and ligand only simulation

[Kavyashree M]

Ok thank you. I thought it was for protein-ligand-water
that needs to be rerun without PME.

Thanks
Regards
Kavya



On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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