Re: constraints im molecular dynamics



>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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