Scalable Software Services for Life Science

VOTCA

VOTCA is a Versatile Object-oriented Toolkit for Coarse-graining
Applications. Coarse-grained (CG) simulations are an important tool to
investigate systems on larger time and length scales. Several methods for
systematic coarse-graining were developed, varying in complexity and the
property of interest. Thus, the question arises which method best suits a
specific class of system and desired application. The main objective of VOTCA is
to provide a uniform platform for coarse-graining methods and to allow direct
comparisons of the methods.

VOTCA was introduced in 2009 by theoretical group of Prof. Kurt Kremer at MPI-P,
Mainz, Germany [J. Chem. Theor. Comp. 2009, vol. 5(12), p. 3211], and now it is
further being developed at University of Illinois at Urbana-Champaign, USA and
Los Alamos National Lab., NM, USA.  It is available for free as a open source
software. The core of VOTCA is developed using C++ and the C++ core is
interfaced to bash and perl-flow-control scripts. The source code of VOTCA is
currently being hosted on googlecode at https://code.google.com/p/votca/ and its
homepage is http://www.votca.org/ . Along with the source-code, the googlecode
and homepage sites of VOTCA also contain user manuals, tutorials, and code
documentations.

The coarse-graining methods available in the last stable release of the VOTCA,
1.2.3, are the Boltzmann inversion, iterative Boltzmann inversion, inverse Monte
Carlo, and force-matching, and the interface to GROMACS is provided to carry out
MD simulations required for coarse-graining. We continue to work on improving
the VOTCA package, and design and add new methods to VOTCA. Recently, we have
added two new methods, namely relative entropy and simple-based optimization
methods. In additions to newly implemented methods, we have implemented parallel
analysis framework to improve the performance of VOTCA by use of HPC hardware,
and have also added interfaces to LAMMPS, Espresso, Espresso++, and DLPOLY to
complement the existing GROMACS interface.

AttachmentSize
votca-tools-1.2.4_pristine.tgz82.85 KB
votca-tools-1.2.4.tgz953.58 KB
votca-csgapps-1.2.4.tgz9.99 KB
votca-csg-tutorials-1.2.4.tgz3.55 MB
votca-csg-manual-1.2.4.pdf1005.01 KB
votca-csg-1.2.4.tgz183.93 KB