[gmx-users] Problem with PME in LIE

Justin Lemkul jalemkul at vt.edu
Wed Jul 17 16:46:59 CEST 2013



On 7/17/13 10:43 AM, Sainitin Donakonda wrote:
> Ok..thanks...so i will use -rerun option in final production ..step..as
> follows...actually i ran 20 ns MD simulation so i used extend option to run
> everything in cluster in correct time
>
> #first 10 ns
>
> grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
> MD_10.tpr
>
> mdrun -s MD_10.tpr *-rerun MD_20* -deffnm MD_10
>
> #extension for 10 more ns
>
> tpbconv -s MD_first10.tpr -extend 10000 -o md_extended_2.tpr
>
>   mdrun -s md_extended_2.tpr -deffnm MD_second10 *-rerun MD_second10* -cpi
> MD_first10.cpt -np 32
>
> Can you please tell is this commands are appropriate for production run
> using -rerun option...in help manual it is mentioned that "Neighbor

You will need a new .tpr file that does not use PME.  Then, I would suggest 
concatenating the existing .xtc files to streamline the process.  I also do not 
recall whether the -rerun option works in parallel, but in any case it is 
reasonably fast even in serial.  Thus:

mdrun -s newtpr.tpr -rerun full20ns.xtc

> searching will be performed for every frame, unless nstlist is zero"..
> should i set nslist to zero in MDP file?
>

No.  You want the neighbor list to be updated at every frame in the .xtc, 
otherwise you will miss interactions and the output will likely be flawed.

-Justin

> Thanks
>
>
> On Wed, Jul 17, 2013 at 4:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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<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 <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

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



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