Search Results for "linux distribution 2017"

.... Chem. Theory Comput. 11 (2015), 2517-2524 L.C.Kröger, W.A.Kopp, M.Döntgen, K.Leonhard, "Assessing Statistical Uncertainties of Rare Events in Reactive Molecular Dynamics Simulations", J. Chem. Theory Comput. 13 (2017), 3955-3960 M.Döntgen, F.Schmalz, W.A.Kopp, L.C.Kröger, K.Leonhard, "Automated Chemical Kinetic Modeling via Hybrid Reactive Molecular Dynamics and Quantum Chemistry Simulations", J. Chem. Inf. Model. 58 (2018), 1343-1355 Check the Wiki for bug reports and fixes.

News: active RMG development has moved to github https://github.com/RMGDFT News: V4.1.0 released on 09/29/2020 News: V4.0.0 released on 09/01/2020 with major updates. News: V3.0.0 released on 06/09/2018 with major updates. News: V2.2.2 released on 10/14/2017 with minor bug fixes. News: V2.2 with performance enhancements, bug fixes and new features released on 06/26/2017. Sources are available with binaries to follow soon. News: V2.1 with many improvements released on 07/15/2016. Sources...

... of molecule-water complexes with graphical user interface (GUI), 2) semi-automatic frequency analysis using symbolic potential energy distribution matrix and comparison of optimized internal coordinates, 3) GUI for charge fitting with three modes: manual, Monte-Carlo sampling or brute force, and 4) GUI for dihedral terms fitting. The usage of these tools decreases the labor effort, lowers manual input errors and reduces the time needed for accurate MM parameterization efforts.

The program Orthos is developed to performed simulation (including nonlinear least-squares fitting) of EPR spectra of nitroxide biradicals. The program capabilities include simulation of rigid-limit and slow-motional spectra, of both isotropic and aligned samples. The spectra of multiple paramagnetic species, both bi- and monoradicals can be modeled. NB: Please note that now (as of Nov 2016) the distribution is being updated so that to improve reliability, OS-universality, and the quality...

DISCUS is a set of programs to simulate the atomic structure of disordered materials and calculate experimental properties such as diffuse scattering or the atomic pair distribution function.

trj_cavity finds protein cavities throughout Molecular Dynamics (MD) simulation trajectories. The program works with files in PDB format, but it also can read/generate GROMACS compatible formats such as XTC. The same project can be compiled as a GROMACS tool or as a standalone version. Installation instructions are provided in the INSTALL file of the project and in https://sourceforge.net/p/trjcavity/wiki/Home/#ffad If you need support using this tool (or report bugs), please post it in...

A collection of cheminformatics and machine-learning software written in C++ and Python. NOTE: the RDKit source code and downloads are now in github: https://github.com/rdkit/rdkit The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity...

... of deuterium incorporation from a spectrum with isotopic fine structure resolved. Given a peptide sequence or elemental formula, the distribution of deuterium-associated mass-to-charge ratios is calculated based on a particular charge state corresponding to the molecular species resolved in an input mass spectrum. Peaks in the input mass spectrum fitting within bins corresponding to these values are used to determine the distribution of deuterium incorporated.

Alchemy Linux is a Linux distribution (based on Fedora) for chemists (and mathematicians and physicists). This remix comes with a whole set of packages to help with experiments, simulations and publications. (This project is not maintained or endorsed by Red Hat or the Fedora project).

NanoHive is a modular simulator used for modelling the physical world at a nanometer scale. The intended purpose of the simulator is to act as a tool for the study and development of nanotech entities. The project will also focus on the simulation of complex biological applications such as Targeted Drug Delivery by simulating nanowires, magnetic nanoparticles and others. Updates will follow from January 2017.

iso2l (ˈaisəutuːl, spoken isotool) is a software to calculate the isotopic distribution of a chemical formula or a amino acid chain. The development has been MOVED TO https://github.com/binfalse/iso2l

Ion Chromatography Data Analyzer for analyzing wasted oil. Can parse data file from HW2000 workstation.

SpecMark (spectral Markov) is a method for calculating the joint probability distribution over species in a regulatory network.

ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.

The ISOTOPIC PATTERN CALCULATOR is a small linux tool for mass spectrometry. It calculates the isotopic distribution for a given chemical formula or peptide sequence. GIPS is a GUI Version of the Isotopic Pattern Calculator.