Paper Citing NAMD - Abstract
Bonomi, Massimiliano; Branduardi, Davide; Bussi, Giovanni; Camilloni, Carlo; Provasi, Davide; Raiteri, Paolo; Donadio, Davide; Marinelli, Fabrizio; Pietrucci, Fabio; Broglia, Ricardo A.; Parrinello, Michele
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
COMPUTER PHYSICS COMMUNICATIONS, 180:1961-1972, OCT 2009
Here we present a program aimed at free-energy calculations in molecular systems. it consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both Fortran and C/C++ codes. Program summary Program title: PLUMED Catalogue identifier: AEEE_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v1_0.html Program obtainable fro m: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Lesser GPL No. of lines in distributed program, including test data, etc.: 107 505 No. of bytes in distributed program, including test data, etc.: 2 052 759 Distribution format: tar.gz Programming language: ANSI-C Computer: Any computer capable of running an executable produced by GCC compiler Operating system: Linux/Unix RAM: Depending on the number of atoms, the method chosen and the collective variables used Classification: 23 External routines: Must be interfaced with a MD code (such as GROMACS, NAMD, DL_POLY or SANDER). Nature of problem: Calculation of free-energy surfaces for biological and condensed matter systems. Solution method: Implementation of various enhanced sampling techniques. Unusual features: PLUMED is not a stand-alone program but it must be interfaced with a MD code (such as GROMACS, NAMD, DL_POLY or SANDER) that needs to be recompiled. Each interface is provided in a patch form. Running time: Depending on the number of atoms, the method chosen and the collective variables used. (C) 2009 Elsevier B.V. All rights reserved.
