[gmx-users] Problem with PME in LIE

[Sainitin Donakonda]

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?

Thanks,
Nitin



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
>> electrostatics..
>>
>> 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
>
> --
> ==============================**====================
>
> 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)
> 706-7441
>
> ==============================**====================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>