Subject: Re: CCL:Programs that can perform MD only in torsional space

From: <[email-masked]>
Date: Mon, 29 Jun 1998 17:51:24 +0200 (DFT)

> I want to know if there exists one program that can perform Molecular
> Dynamics Simulation only in torsional space. I also want to know related
> algorithms and the degree of difficulty to implement such a program compared
> with normal Cartesian MD programs. I know some programs can do this by

You might be interested in these two papers:

    G.R. Kneller, K. Hinsen
    Generalized Euler equations for linked rigid bodies
    Phys. Rev. E 50, 1559 (1994)

    K. Hinsen, G.R. Kneller
    Influence of constraints on the dynamics of polypeptide chains
    Phys. Rev. E 52, 6868 (1995)

The first paper derives the equations of motions for a system with
arbitrary distance constraints using generalized coordinates (torsion
angle dynamics is a special case). The second paper presents an
implementation and application. The implementation is available as a
set of Fortran subroutines that should be easy to integrate into any
MD program (we used an old version of Gromos); write to me if you are
interested. Please note that I didn't spend much effort to optimize
the implementation. In my experience, constraint-type dynamics, in
whatever way it is implemented, does not work well for significantly
reduced coordinate sets, and is of little advantage for
almost-complete coordinate sets, so I didn't want to invest any more
effort.

Another paper that could be of interest for you is

    L.M. Rice, A.T. Br"unger
    Torsion Angle Dynamics: Reduced Variable Conformational
    Sampling Enhances Crystallographic Structure Refinement
    Proteins 19, 277 (1994)

It describes protein dynamics in phi-psi space (i.e. a subset of
torsional angle space) for use in structure refinement, i.e. simulated
annealing. For that application, the correctness of the dynamics is
unimportant, so rather drastic constraints can be useful. But then
you might be better off with some Monte-Carlo method if you don't
care about dynamics. I suppose this method is implemented in some
version of XPlor.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: [email-masked]
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------