Search Results for "alpha linux"

Note: This package has been superseded by a Python-only package. See https://github.com/ulflor/wavepacket for the follow-up project. WavePacket is a program package for numerical simulation of quantum-mechanical wavepacket dynamics of distinguishable particles. It can be used to solve single or coupled time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations. Optionally accounting for the interaction with external electric fields within the semiclassical...

ED Software project contains several programs used (mostly) for processing gas-phase electron diffraction (GED) experimental data.

Given dynamical coefficients and/or derivatives of the ionic potential with respect to normal (harmonic) vibrational modes, compute anharmonic energies and electric dipole-permitted transitions and intensities using nearly-degenerate perturbation theory (i.e. properly accounting for Fermi and Darling-Dennison resonances).

RERun is a software tool for creating virtual agarose electrophoresis gels of nucleic acid fragments (restriction digests, PCR amplicons, etc). It is written in Perl and developed on Linux, although it can be made to run on Windows with some work (undocumented).

Magnetic Drug Targeting (MDT) simulation and visualization in traversal and longtitudinal mode.

Project for develop force fields with using ab-initio calculations

Quantum Chemistry Import Tool is a django application that parses the output file of quantum chemistry software as NWChem, Octopus, Gaussian, etc. The result can be saved in relational database.

The basis sets included with ECCE have -- as far as I can tell -- not been updated for many years. In addition, many of the newer basis sets that come with nwchem aren't included, such as the def2- series. nwbas2ecce is a python script that aims to automate as much as possible of the conversion process of a nwchem basis set file into the files necessary for ECCE to included it in the basis set tool. The process isn't completely automatic, but I also believe that it shouldn't be to...

is a interactive molecular visualisation program designed especially designed for coarse-grained simulation of non-spherical particles. Ellipsoids (Gay-Berne), disks, and custom shaped uniaxial particle (e.g. pear-shaped particles) can be represented.

BLOSpectrum tools provide programs to automatically classify proteins according to SCOP database. In order to achieve such a goal, they implements all the required information theory widgets on BLOSpectrum fingerprints.

NOSE is a package for simulation of linear and non-linear optical and infrared spectra, including absorption, fluorescence, circular dichroism, pump-probe, photon echo and other.

The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!

CoCOOT is an extended collaboration system of COOT(Crystallographic Object Oriendted Toolit). It operates an add-on of original Coot. It enables to collaboration through internet.

Vimes: Visual interface to materials simulations - An open source, python/Open GL interface to molecular and materials simulation programs

cnsFace is a GUI for the Crystallography and NMR System.

GParticles is a tool to simulate the growth behaviour of two- and three-dimensional nano particles based on a simple grid model, with adjustable (time-dependent) concentrations of the particle's different components.

Agent-based multiscale model of cancer proliferation dynamics

QRasMol is a reimplementation of RasMol in C++ with updated CMake build systems.

PepArML: An unsupervised, model-free, combining peptide identification arbiter for tandem mass spectra via machine learning.

Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.

Ninja is an object oriented toolkit for manipulating InChI identifiers.

Mito-MAS-m is a simulator of the mitochondrial inner membrane and the enzymatic complexes embedded in it, implementing a coarse-grained (CG) model of the molecules using rigid structures and Dissipative Particules Dynamics (DPD) as motion equation.