From csoares@iris1.Fki.UU.SE Mon Nov 8 15:47:13 1993 Received: from iris1.FKI.UU.SE by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/BelWue-1.0SG(subsidiary)) (for ferenc) id AA10996; Mon, 8 Nov 93 15:47:13 +0100 Received: from [130.238.69.55] (Mac55.FKI.UU.SE) by iris1.Fki.UU.SE with SMTP id AA14492 (5.67a8/IDA-1.5 for ); Mon, 8 Nov 1993 15:22:16 GMT Date: Mon, 8 Nov 1993 15:22:16 GMT Message-Id: <199311081522.AA14492@iris1.Fki.UU.SE> To: ferenc From: csoares@iris1.fki.uu.se Subject: Re: constraints im molecular dynamics Cc: csoares@iris1.fki.uu.se Status: RO >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 ----------------------------------------------------------------- I Claudio Soares I MOLECULAR MODELLING I I Uppsala University I GROUP I I Dep.Physical Chemistry I I I Box 532 I : I I S-751 21 Uppsala I l I I SWEDEN I C=O I I I l I I Pho: +46 18 183631 I H-N I I Fax: +46 18 508542 I l I I Email:CSOARES@IRIS1.FKI.UU.SE I : I -----------------------------------------------------------------