[gmx-users] Problem with PME in LIE

[Sainitin Donakonda]

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

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
>>>>>
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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
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>>> 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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