[gmx-users] Problem with PME in LIE

[Sainitin Donakonda]

Usually i collect data after final production run...after this i take .xtc
file and analyze it using various gromacs tools ..

thanks,
nitin


On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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?
>
> -Justin
>
>  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 <jalemkul at outerbanks.umaryland.edu>> | (410)
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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 <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
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