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.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.