Search Results for "python source codes"

ERmod (Energy Representation Module) is a program to calculate the solvation free energy based on the energy representation method (J. Chem. Phys. 113, 6070 (2000)). The program allows users to calculate the solvation free energy to arbitrary solvents, including inhomogeneous systems, and can run in cooperation with state-of-art molecular simulation software, such as LAMMPS, GROMACS and/or AMBER.

We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and...

This software has moved to http://www.poissonboltzmann.org/.

Atomistic NanoTransport (ANT) comprises a series of codes designed to compute electronic quantum transport with a broad range of applicability in nanoelectronics. ANT.Gaussian (or ANT.G for brevity) relies on the popular quantum chemistry code GAUSSIAN03/09 code with which interfaces in a seamless manner. Straightforwad use of ANT.G include the computation of the zero-bias conductance (or, alternatively, the electrical current under an applied bias voltage) of a variety of nanoscale systems...

MDcons is a tool to analyze conserved contacts during Molecular Dynamics (MD) simulations of Protein, Rna, Dna & Ligand based complexes. The input is either a Molecular Dynamics trajectory or a set of snapshots. The input can also be a single snapshot. The outputs are (1) map of most/less frequently conserved contacts during MD (2) a list of most/less frequently conserved contacts during MD.

Larch is a scientific data processing language that is designed to be easy to use for novices and complete enough for advanced data processing and analysis. Larch provides a wide range of functionality for dealing with arrays of scientific data, and basic tools to make it easy to use and organize complex data. Larch has been primarily developed for dealing with x-ray spectroscopic and scattering data, especially the kind of data collected at modern synchrotrons and x-ray sources. ...

SMMP (Simple Molecular Mechanics for Proteins) is a program library for protein simulations with an emphasis on advanced Monte Carlo algorithms. It includes various force fields to calculate the energy of a protein and protein-protein interactions.

Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.