AMBER Archive (2008)

Subject: Re: AMBER: SMD RESTRAINTS

From: fatima.chami_at_durham.ac.uk
Date: Thu Jun 12 2008 - 12:07:49 CDT

Quoting Adrian Roitberg <roitberg_at_qtp.ufl.edu>:

>
> Fatima,
> You cannot at this time do this.
> We are working on code to do it as we speak. If you know enough fortran
> you can go into src/sander/nmr.f and add this yourself
> for your particular case. We want to make it more general.

Thanks for replying
according to this communication : "J.AM.CHEM.SOC.2005,127, 6940 "which is cited
as ref 141 in Amber 9 manual .. the reaction coordinate was a distance difference

what about using umbrella sampling ..would that be possible

fatima

>
> One option is to do a 2-D umbrella scan for the two distances.
>
> Cheers
> Adrian
>
>
> fatima.chami_at_durham.ac.uk wrote:
> > Dear folks
> >
> > In a steered MD:
> > the reaction coordinate is a difference between two distances ..how can i
> set up
> > such a restraint. Jar =1 does not allow more than one restraint
> >
> > any example of doing this
> > best wishes
> > Fatima
> >
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>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project
> Department of Chemistry
>
> Senior Editor. Journal of Physical Chemistry
> American Chemical Society
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
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> 

-- 
Dr. F.Chami
Science Lab.
Department of Chemistry
Durham University
South Road Durham, DH 1 4 LE
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