PLUMED 2: New feathers for an old bird

作者：Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide; Camilloni, Carlo; Bussi, Giovanni^*

来源：Computer Physics Communications, 2014, 185(2): 604-613.

DOI：10.1016/j.cpc.2013.09.018

• Free energy
• Molecular dynamics
• Enhanced sampling
• Dimensional reduction

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.

• 出版日期2014-2