[gmx-users] Problem with PME in LIE
Sainitin Donakonda
saigro16 at gmail.com
Wed Jul 17 16:54:39 CEST 2013
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 ?
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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