Ok I will do it in parts with smaller interval.
> On Mon, Apr 18, 2011 at 10:19 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>> Thanks Jason for reply.
>>
>> Actually it is very time comsuming process and I am running it in cluster
>> if
>> some how job will be terminated
>> then it will be problematic.
>> So I have taken interval 10,should I take interval of 5 or more smaller.
>>
>> I am studying water mediated H-bonding I have total of 4ns trajectory and
>> form
>> start to upto 2500ps
>> water mediated interaction is exiting.
>>
>> > Hello,
>> >
>> > I'm guessing you won't see much difference between 250 frames and 1250
>>
>>
>> Sorry here I didnt get if here is no diffrence between 250 (when intervalis
>> 10)
>> and 1250(when interval is 1)
>> frames then where is the problem?
>>
>
> What I mean is there's little benefit to doing 1250 frames instead of 250,
> since your final answer is unlikely to change.
>
> All the best,
> Jason
>
>
>>
>> > frames that are spread over the length of the same trajectory.
>> >
>> > In any case, you can always separate it into 2 simulations as long as you
>> > combine the statistics at the end.
>> >
>> > Hope this helps,
>> > Jason
>> >
>> > On Mon, Apr 18, 2011 at 1:31 AM, Sangita Kachhap <sangita.imtech.res.in
>> >wrote:
>> >
>> >>
>> >> Hello all
>> >>
>> >> I have to do MMPBSA_Nmode analysis and I have trajectory of 2500 frames.
>> >> I want to use interval=10 so that total frames will be 250 for nmode
>> >> calculation
>> >> and
>> >> run it on 25 processor,calculated time of run is aprrox 10 days.
>> >>
>> >> Here I want to do nmode calculation two times,1250 frames at a time so
>> >> total
>> >> frames will be 2500.
>> >>
>> >> Will it be relavent to divide total frames into two run?
>> >>
>> >> With regard
>> >>
>> >> Sangita Kachhap
>> >> JRF
>> >> BIC,IMTECH
>> >> CHANDIGARH
>> >>
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>> >
>> > --
>> > Jason M. Swails
>> > Quantum Theory Project,
>> > University of Florida
>> > Ph.D. Candidate
>> > 352-392-4032
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> With regard
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Mon Apr 18 2011 - 11:00:04 PDT
