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Reduced variable molecular dynamics
Author(s) -
Turner James,
Weiner Paul,
Robson Barry,
Venugopal Ravi,
Schubele Harry,
Singh Ramen
Publication year - 1995
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540161009
Subject(s) - constraint (computer aided design) , computer science , molecular dynamics , process (computing) , trajectory , variable (mathematics) , algorithm , extension (predicate logic) , mathematical optimization , chemistry , mathematics , computational chemistry , mathematical analysis , physics , geometry , astronomy , programming language , operating system
This article describes an extension to previously developed constraint techniques. These enhanced constraint methods will enable the study of large computational chemistry problems that cannot be easily handled with current constrained molecular dynamics (MD) methods. These methods are based on an O ( N ) solution to the constrained equations of motion. The benefits of this approach are that (1) the system constraints are solved exactly at each time step, (2) the solution algorithm is noniterative, (3) the algorithm is recursive and scales as O ( N ), (4) the algorithm is numerically stable, (5) the algorithm is highly amenable to parallel processing, and (6) potentially greater integration step sizes are possible. It is anticipated that application of this methodology will provide a 10‐ to 100‐improvement in the speed of a large molecular trajectory as compared with the time required to run a conventional atomistic unconstrained simulation. It is, therefore, anticipated that this methodology will provide an enabling capacity for pursuing the drug discovery process for large molecular systems. © 1995 John Wiley & Sons, Inc.