Paper Citing NAMD - Abstract
Limbach, H.J.; Arnold, A.; Mann, B.A.; Holm, C.
ESPResSo - an extensible simulation package for research on soft matter systems
COMPUTER PHYSICS COMMUNICATIONS, 174:704-727, MAY 1 2006
We describe a new program package that is designed to perform numerical Molecular Dynamics (MD) and Monte Carlo (MC) simulations for a broad class of soft matter systems in a parallel computing environment. Our main concept in developing ESPResSo was to provide a user friendly and fast simulation tool which serves at the same time as a research platform capable of rapidly incorporating the latest algorithmic developments in the field of soft matter sciences. A particular strength of ESPResSo is its efficient treatment of long range interactions for various geometries using sophisticated algorithms like P(3)M, MMM2D, MMM1D and ELC. It is already equipped with a broad variety of interaction potentials, thermostats, and ensemble integrators; it offers the usage of constraints, masses and rotational degrees of freedom; it allows to move between different ensembles on-the-fly. An efficient MPI parallelization allows the usage of multi-processor architectures. Strict usage of ANSI-C for the core functions and a Tcl-script driven user interface makes ESPResSo platform independent. This also ensures easily modifiable interfaces to communicate with other MD/MC Packages, real-time visualization and other graphic programs. We tried to maintain a clear program structure to keep ESPResSo extensible for future enhancements and additions. ESPResSo is implemented as an open source project with the goal to stimulate researchers to contribute to the package. (C) 2005 Elsevier B.V. All rights reserved.
