AMBER Archive (2002)

Subject: Re: timings?

From: David A. Case (case_at_scripps.edu)
Date: Fri Dec 06 2002 - 09:46:27 CST

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://structbio.vanderbilt.edu/hypermail/amber-archive/2877.phtml

You could find this and other answers by doing a google search on the
Amber web site archives:

     minimization site:structbio.vanderbilt.edu

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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