[gmx-users] Problem with PME in LIE
Justin Lemkul
jalemkul at vt.edu
Wed Jul 17 16:56:02 CEST 2013
On 7/17/13 10:54 AM, Sainitin Donakonda wrote:
> I started MD very recently dont have much experience you said i would need
> .tpr file which doesnot use PME ? how can i get that ?
>
By writing a new .mdp file that doesn't use PME. Please refer to previous
discussions on this topic. People ask about LIE frequently, and for some reason
there seems to be a rash of interest lately...
-Justin
> Thanks,
> Nitin
>
>
> On Wed, Jul 17, 2013 at 4:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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.**umaryla**nd.edu<http://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<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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