Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] aeee_v2_0.tar.gz(6509 Kbytes)|
|Manuscript Title: PLUMED 2: New feathers for an old bird|
|Authors: Gareth A Tribello, Massimiliano Bonomi, Davide Branduardi, Carlo Camilloni, Giovanni Bussi|
|Program title: PLUMED 2|
|Catalogue identifier: AEEE_v2_0|
Distribution format: tar.gz
|Journal reference: Comput. Phys. Commun. 185(2014)604|
|Programming language: ANSI-C++.|
|Computer: Any computer capable of running an executable produced by a C++ compiler.|
|Operating system: Linux operative system, Unix OS-es.|
|Has the code been vectorised or parallelized?: Yes, parallelized using MPI.|
|RAM: Depends on the number of atoms, the method chosen and the collective variables used.|
|Keywords: Free Energy, Molecular Dynamics, Enhanced Sampling, Dimensional Reduction.|
|PACS: 87.10.Tf, 87.15.ap, 31.15.xv, 36.20.Ey.|
|Classification: 3, 7.7, 23.|
External routines: GNU libmatheval, Lapack, Blas, MPI
Does the new version supersede the previous version?: This version supersedes the previous version for the most part. There are a small number of very specific situations where the previous version is better, due to performance or to non ported features. We are actively working on porting these last few features into the new code.
Nature of problem:
Calculation of free-energy surfaces for molecular systems of interest in biology, chemistry and materials science, on the fly and a-posteriori analysis of molecular dynamics trajectories using advanced collective variables
Implementations of various collective variables and enhanced sampling techniques.
Reasons for new version:
The old version was difficult to maintain and its design was not as flexible as this new version. This lack of flexibility made it difficult to implement a number of novel methods that have emerged since the release of the original code.
Summary of revisions:
The new version of the code has a completely redesigned architecture, which allows for several important enhancements. This allows for a much simpler and robust input syntax and for improved performance. In addition, it provides several, more-complex collective variables which could not have been written using the previous implementation. Furthermore, the entire code is fully documented so it is easier to extend. Finally, the code is designed so that users can implement new variables directly in the input files and thus develop bespoke applications of these powerful algorithms.
PLUMED 2 can be used either as a standalone program, e.g. for a-posteriori analysis of trajectories, or as a library embedded in a Molecular Dynamics code (such as GROMACS, NAMD, Quantum ESPRESSO, and LAMMPS). Interface with these software is provided in a patch form. Library is documented to ease its embedding into other software.
The distribution file contains a test suite, user and developer documentation and a collection of patches and utilities.
Depends on the number of atoms, the method chosen and the collective variables used. The regression test suite provided takes approximately 1 minute to run.
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