Paper Citing NAMD - Abstract
Moskovsky, A.A.; Vanovschi, V.V.; Konyukhov, S.S.; Nemukhin, A.V.
Implementation of the replica-exchange molecular dynamics method for rigid bodies
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 106:2208-2213, AUG 15 2006
We describe an implementation of the replica-exchange molecular dynamics (REMD) algorithm for rigid-body molecular dynamics targeting its application in the flexible effective fragment quantum mechanical-molecular mechanical (QM/MM4) method. The main objective of the stage of the project is to obtain an efficient minimization tool for the MM subsystem. The computer program developed allows one to carry out calculations of molecular dynamics trajectories for atomic particles and for rigid bodies at constant temperature, using the chain Nose-Hoover thermostat. For REMD calculations, the OpenTS dynamic parallelization is used, which allows one to run simulations either on single computational clusters or on meta-clusters. A two-level parallelization scheme has been implemented, assuming that both REMD (upper level) and individual molecular dynamics trajectories (lower level) are parallelized. Structures of small and large water clusters as well as protein conformations are considered as first applications. (c) 2006 Wiley Periodicals, Inc.
