AMBER Archive (2005)

Subject: Re: AMBER: big fluctuation in MM-PBSA/GA

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Fri Apr 15 2005 - 13:59:09 CDT

On 4/15/05, Xin Hu <hux_at_mail.rockefeller.edu> wrote:
> >
> > A snapshot was taken every 2ps for binding energy calculation
> > (according to Tutorial_03). Here is the statistics.out.
> >
>
> Hi Eric,
> I am a newer of MM_PBSA. What's the tutorial_03?

/amber8/src/mm_pbsa/Examples/03_MMPBSA_Binding/

> You have a 10ns simulation and take the snapshot every 2ps, so you used 5000
> snapshot for the binding energy calculation? From Dr. Gohlke recent paper,
> it seems 100-200 snapshoots are enought to generate the meaningful
> calculation?
Yes, besides making sure the system is at stable condition, longer
simulation with more snapshots will only help to reduce the standard
error of the mean since the STD remains big and is divided by the sqrt
of the number of snapshots.

Eric
>
> Thanks for help,
>
> Xin
>
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