On the basis of the molecular dynamics algorithm proposed by Kalibaeva et al. [G. Kalibaeva, M. Ferrario, G. Ciccotti, Mol. Phys. 101 (2003) 765.] for systems with holonomic constraints in isobaric-isothermal ensemble, we discuss a new recursive algorithm which eliminates the inconsistency associated with the double calculation of constraint forces present in RATTLE. The algorithm is tested on bulk water and on a system containing a polymer with a large number of constraints to evaluate the CPU gain with respect to the usual RATTLE algorithm. (c) 2006 Elsevier Inc. All rights reserved.

Trotter derived algorithms for molecular dynamics with constraints: Velocity Verlet revisited / V., Marry; Ciccotti, Giovanni. - In: JOURNAL OF COMPUTATIONAL PHYSICS. - ISSN 0021-9991. - STAMPA. - 222:1(2007), pp. 428-440. [10.1016/j.jcp.2006.07.033]

Trotter derived algorithms for molecular dynamics with constraints: Velocity Verlet revisited

CICCOTTI, Giovanni
2007

Abstract

On the basis of the molecular dynamics algorithm proposed by Kalibaeva et al. [G. Kalibaeva, M. Ferrario, G. Ciccotti, Mol. Phys. 101 (2003) 765.] for systems with holonomic constraints in isobaric-isothermal ensemble, we discuss a new recursive algorithm which eliminates the inconsistency associated with the double calculation of constraint forces present in RATTLE. The algorithm is tested on bulk water and on a system containing a polymer with a large number of constraints to evaluate the CPU gain with respect to the usual RATTLE algorithm. (c) 2006 Elsevier Inc. All rights reserved.
2007
algorithms; holonomic constraints; molecular dynamics
01 Pubblicazione su rivista::01a Articolo in rivista
Trotter derived algorithms for molecular dynamics with constraints: Velocity Verlet revisited / V., Marry; Ciccotti, Giovanni. - In: JOURNAL OF COMPUTATIONAL PHYSICS. - ISSN 0021-9991. - STAMPA. - 222:1(2007), pp. 428-440. [10.1016/j.jcp.2006.07.033]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/33063
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