AMBER Archive (2003)

Subject: Re: AMBER: Sander / Anal

From: David A. Case (case_at_scripps.edu)
Date: Mon Dec 01 2003 - 14:58:32 CST

On Mon, Dec 01, 2003, Emmanuel Giudice wrote:
>
> I'm comparing the energy output of Sander and anal. To do so I have
> performed with sander a "single point" energy calculation in vacuo on a
> very simple system...

>
> Here is my input file for Sander
>
> &cntrlHere is my input file for Sander
> imin=0, ntx=1, ntpr=1, ntwr=1, ntwx=1, ntwe=1,
> nscm=5000,
> ntf=2, ntc=2,
> ntb=0, igb=2
> nstlim=1, t=0.0, dt=0.002,
> cut=999.0,
> irest=0
> &end
> -----------------------------------------------------------------------------
>

All components of your energy are different, so my guess is that you are not
extracting the intial (step 0) results from sander. It's easier to set
imin=1 and maxcyc=1 to ensure you are using the same coordinates.

Also, you should turn off shake (set ntf=ntc=1), since anal also doesn't know
about shake.

..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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