[gmx-users] g_lie and ligand only simulation

[Kavyashree M]

Dear users,

When the simulation was carried out with PME
rcoulomb was set equal to rlist. But when I need to
to ligand-water simulation without PME (with RF-0)
then it requires rlist greater by 0.1-0.3 than rcoulomb.
So if I rerun protein-ligand-water simulation there
could be more differences in the energies isnt it?

Thank you
Regards
Kavya


On Sat, Nov 2, 2013 at 9:51 PM, Kavyashree M <hmkvsri at gmail.com> wrote:

> 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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>
>