[gmx-users] Problem with PME in LIE
jalemkul at vt.edu
Wed Jul 17 15:51:49 CEST 2013
On 7/17/13 9:21 AM, Sainitin Donakonda wrote:
> Hi justin,
> Thanks for explaination .. i already ran MD for both ligand alone and
> protein ligand complex..
> So now can you please tell me where should use mdrun -rerun option ..i mean
> at which stage ..should i used in Energy miniminimzation or NVT and NPT
> equilibration or Production run ..
> Or should i use mdrun -rerun option at every stage ...? or it should be
> used only at final production run?
Which simulation stage do you normally use to collect data?
> On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 7/17/13 8:54 AM, Sainitin Donakonda wrote:
>>> Hi ,
>>> I want to use g_lie for my protein-drug complex to get binding energy ..i
>>> read some information that we need take care some issues if we used PME
>>> Indeed i have used PME in my simulation..
>>> Can any body explain which parameters to be taken care while running g_LIE
>>> and what is the isssue with PME ..
>> The long-range mesh terms are not decomposable in a pairwise manner. LIE
>> assumes that all of your interactions can be broken down from additive
>> terms, and this is not the case with PME.
>> and why we should use -rerun option beofre running LIE
>> If you evaluate the energies from a PME simulation, the result will be
>> off. If you use plain cutoffs for the dynamics, the simulation will
>> probably be junk. So one solution is to run the simulation with PME to get
>> reasonable dynamics, then post-process via mdrun -rerun while evaluating
>> energies with plain cutoffs (which one would usually increase beyond normal
>> values, IIRC, but I do not use LIE myself).
>> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
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Justin A. Lemkul, Ph.D.
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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