Subject: Add: Re: CCL:complex geom calc protocol

From: val <[email-masked]>
Date: Thu, 14 Jan 1999 12:17:12 +0300

> To: Goutam Das <[email-masked]>
> Subject: Global Minima
> 
> Dear Dr. Das,
> 
> I do not have the reference on hand, but I do know that in the late 80's
> Dr. Scheraga published a paper on an algorithm for finding the global
> minimum for a geometry by manipulating the dimensionality of the
> problem. I believe instead of working in n-space and doing a geometry
> minimization (which is almost guaranteed to NOT find the global
> minimum), Scheraga's approach (I believe, check the paper) works on
> starting with a low dimensionality then adding complexity, the idea
> being that if you approach the problem from the downside, the first
> point you should hit would be the global minimum...
> 
> Good luck finding the reference. If I manage to run across it I will
> send it to you.
> 
> Best of luck in your research!
> --
> *********
> Mark A. Zottola                       Alabama Research and Education Network

 It seems the references are:

 Purishma E.O., Scheraga H.A., "An approach to the multiple-minima 
problem by relaxing the dimensionality", Proc.Nat.Acad.Sci. U.S.A.,
1986,83,2782-2786.

 Purishma E.O., Scheraga H.A.,"An approach to the multiple-minima 
problem in protein folding by relaxing the dimensionality",
J.Mol.Biol., 1987, 196, 697-709.

Also, the following paper may be of interest:

 R.C.van Schaik, H.J.Berendsen, A.E.Torda, W.F.van Gunsteren, "A structure
refinement method based on molecular dynamics in four spatial dimensions",
J.Mol.Biol., 1993, 234, 751-762.

 The last method is implemented in the GROMOS package:
                  http://igc.ethz.ch/gromos/

                                              best regards,
                                              Valentin.

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