[gmx-users] Problem with PME in LIE

[Justin Lemkul]

On 7/17/13 10:12 AM, Sainitin Donakonda wrote:
> Usually i collect data after final production run...after this i take .xtc
> file and analyze it using various gromacs tools ..
>

And there you have it.  LIE is just an analysis method like anything else. 
There is no purpose in my mind in reanalyzing nonbonded energies during 
equilibration.

-Justin

> 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)
>>>> 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 <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

==================================================