Paper Citing NAMD - Abstract
Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide; Camilloni, Carlo; Bussi, Giovanni
PLUMED 2: New feathers for an old bird
COMPUTER PHYSICS COMMUNICATIONS, 185:604-613, FEB 2014
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field. Program summary Program title: PLUMED 2 Catalogue identifier: AEEE_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Yes No. of lines in distributed program, including test data, etc.: 700646 No. of bytes in distributed program, including test data, etc.: 6618136 Distribution format: tar.gz Programming language: ANSI-C++. Computer: Any computer capable of running an executable produced by a C++ compiler. Operating system: Linux operating system, Unix OSs. Has the code been vectorized or parallelized?: Yes, parallelized using MPI. RAM: Depends on the number of atoms, the method chosen and the collective variables used. Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0. Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961. External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.
