Subject: Re: constraints im molecular dynamics

From: [email-masked]
Date: Mon, 8 Nov 1993 15:22:16 GMT

>Dear Netters!
>
>I am looking for information on methods to impose constraints
>on molecules (constant bond-length etc.) in molecular 
>dynamics simulations.
>
>Does anybody know about a fast constraints-algorithm in connection 
>with Gear's (predictor-corrector) or Verlet's (velocity verlet)
>algorithm.
>
>
>Thanks in advance.
>
>Ferenc
>
>Ferenc Molnar

        The most widely use algorithm for bond length constraints is the
SHAKE algorithm which was initially applied in the framework of the Verlet
algorithm (1) but it can also be incorporated in predictor-corrector
methods (2). The same formulation can be used to other types of
constraints. The GROMOS package has a subroutine to do this (with
Verlet's).
        Hope it helps,

        Claudio

(1) Ryckaert, J.-P., Ciccotti, G., Berendsen, H.J.C. (1977) "Numerical
integration of the cartesian equations of motion of a system with
constrains: Molecular dynamics of n-Alkanes",J.Comp.Phys., 23, 327-341

(2) van Gunsteren, W.F., Berendsen, H.J.C.(1977) "Algorithms for
macromolecular dynamics and constraint dynamics", Mol.Phys., 34, 1311-1327
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---

From: "Eric P. Wallis" <[email-masked]>
Date: Tue, 9 Nov 93 10:30:28 CST

There are two programs that work well with verlet algorithm to constrain 
internal coordinates.  The Shake algorithm (by Ryckaert, Ciccotti, and 
Berendsen; J. Comput. Phys., 23, 327 (1977)) and Rattle 
(Anderson, J. Comput. Phys., 52, 24 (1983)).  They are discussed in
Allen and Tildesley book "Computer Simulations of Liquids".

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