[gmx-users] g_lie and ligand only simulation

[Kavyashree M]

Dear users,

Sorry for repeating the same question. I just wanted to know
whether is it ok if I have rlist > rcoulomb in ligand-water and
prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb
in the original simulation using PME?

Thank you
Regards
Kavya







On Wed, Nov 6, 2013 at 11:52 AM, Kavyashree M <hmkvsri at gmail.com> wrote:

> 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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>>
>>
>