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
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Received on Mon Apr 18 2011 - 11:00:03 PDT
