[gmx-users] Problem with PME in LIE
saigro16 at gmail.com
Wed Jul 17 15:21:04 CEST 2013
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?
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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