AMBER Archive (2002)

Subject: Re: IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...)

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Thu Aug 29 2002 - 05:54:15 CDT

I put this in. Basically what it does is to carry out
normal minimization as if imin were 1, but rather
than getting coordinates from inpcrd it gets them
from the trajectory file. It then carries out the minimization
for each frame and reports energies. It is up to you
to process the output file, which will have energies for all
structures. Remember that all of the normal minimization
flags still work, such as number of steps, convergence criteria
and so on.
let me know if you have more questions.
Carlos
----- Original Message -----
From: "Michael Jakusch" <michael.jakusch_at_pharma.anbi.ethz.ch>
To: "Amber List" <amber_at_heimdal.compchem.ucsf.edu>
Sent: Thursday, August 29, 2002 3:36 AM
Subject: IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...)

> On Wed, Aug 28, 2002 at 11:36:51AM -0700, Holger Gohlke wrote:
> > If you want to post-process a whole trajectory, you might want to have a
> > look at the IMIN=5 option for sander. I have never used this, so others
> > might know more.
>
> This looks very interesting to me! Can somebody explain what this
> imin=5 option exactly does? I just quickly browsed through the manual,
> but nothing seems to be mentioned there (except "imin=5 ... read in a
> trajectory for analysis").
>
> Michael
>
> --
> Dr. Michael Jakusch
>
> ETH - Swiss Federal Institute of Technology
> Department of Applied Biosciences
> Winterthurerstrasse 190
> CH-8057 Zürich
> Switzerland
> Phone: +41.1.635 60 71
> Fax: +41.1.635 68 84
> email: michael.jakusch_at_pharma.anbi.ethz.ch
>
>