AMBER Archive (2005)

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

From: Xin Hu (hux_at_mail.rockefeller.edu)
Date: Fri Apr 15 2005 - 13:17:28 CDT

>
> 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?
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?

Thanks for help,

Xin

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