On Fri, Dec 06, 2002, Arvid Soederhaell wrote:
>
> I am running minimizations using sander in AMBER7 and these take forever
> compared to doing the same calculation using sander_classic in AMBER6.
> (Forever means that instead of 1 minute it takes 30 minutes) I do not
> understand what has happened. Here is an example of the input:
>
> ----------------------------------------------------------
> &cntrl
> imin=1, scee=1.2,
> ntpr=100, maxcyc=10000,
> cut=9.0,
> dielc=1,
> nsnb=25, ntr=0, drms=0.1,
> ntmin=0, ncyc=10, ntb=0,nmropt=0,
> &end
> --------------------------------------------------------------
Are you running the full 10000 steps in both cases? Seems like a lot
of iterations to be doing for just 1 minute of time in the sander_classic
case.
Be sure to check out the recommendations for non-periodic minimizaiton in
Amber 7:
http://amber.ch.ic.ac.uk/archive/
You could find this and other answers by doing a google search on the
Amber web site archives:
http://amber.ch.ic.ac.uk/archive/
Ewald is not being run for your system: "direct Ewald" just means the direct
(i.e. normal) part of the energy calculation.
..hope this helps...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Fri Dec 06 2002 - 07:46:27 PST
