[AMBER] Fwd: Implicit solvent GB calculation

From: Rubben Torella <rubben.torella.gmail.com>
Date: Mon, 7 Mar 2011 15:04:35 +0000

Dear Amber community,
I'm trying to perform MD simulation in implicit solvent using Generalized
Born approach on a protein-DNA complex.
I followed the tutorial described here (
http://www.uni-koeln.de/themen/chemie/software/amber7/tutorial/gb/gb_tutorial.html)<http://www.uni-koeln.de/themen/chemie/software/amber7/tutorial/gb/gb_tutorial.html>in
order to set-up the calculation.
We are talking about 7637 atoms in the complex.
I launched the calculation on 64 processors (10 ns), but the calculation
seems to me very slow (1.3 ns/day)
Is there something wrong in this approach or is it normal to have this
calculation speed?
I attached you the input of the MD calculation, in order to know if there
are mistakes or there is some flags that slow down the calculation.
Thank you for your help
Rubben


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Received on Mon Mar 07 2011 - 07:30:01 PST
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