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?
> 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
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Received on Mon Apr 18 2011 - 10:30:03 PDT
