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Showing 19 open source projects for "mining software linux"
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LAMMPS
Public development project of the LAMMPS MD software package
LAMMPS is a large-scale classical molecular dynamics simulator for modeling atoms, molecules, coarse-grained particles, and other particle-based systems. It is designed for high-performance computing and can run efficiently on desktops, clusters, and supercomputers. The software is widely used in materials science, chemistry, physics, nanotechnology, soft matter, and computational engineering. It supports many interaction models, including pair potentials, many-body potentials, reactive... -
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GROMACS
Public/backup repository of the GROMACS molecular simulation toolkit
GROMACS is a molecular simulation toolkit focused on high-performance molecular dynamics. It is widely used for biomolecular systems such as proteins, lipids, nucleic acids, solvents, and ligand interactions. The software is optimized for speed and supports modern CPU and GPU acceleration for large and demanding simulations. It includes tools for system preparation, running simulations, trajectory processing, analysis, and workflow automation. GROMACS is especially strong in computational... -
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DL_POLY
General purpose classical molecular dynamics (MD) simulation software
DL_POLY is a general-purpose classical molecular dynamics simulation package developed at Daresbury Laboratory. It has evolved from older replicated-memory designs into a distributed-memory code suitable for modern parallel computing. The software can be built in serial form or with MPI for larger simulations. It is used for molecular modeling in chemistry, physics, materials science, and condensed-matter research. DL_POLY provides a mature simulation environment for studying atomic and... -
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HOOMD-blue
Molecular dynamics and Monte Carlo soft matter simulation on GPUs
HOOMD-blue is a Python-driven particle simulation engine for molecular dynamics and hard-particle Monte Carlo simulations. It was designed from the ground up for GPU acceleration, with a high-performance C++ and CUDA backend. The software is especially useful for nano-scale, colloidal, polymer, soft matter, and materials simulations. Its Python interface lets users build simulation and analysis workflows using familiar scientific Python tools. HOOMD-blue supports efficient parallel execution... -
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ESPResSo
The ESPResSo package
ESPResSo is a simulation package for molecular dynamics and Monte Carlo simulations of soft matter systems. It is designed for coarse-grained and bead-spring models used in physics, chemistry, and molecular biology. The software can model systems such as polymers, colloids, liquid crystals, ferrofluids, DNA, lipid membranes, and other complex fluids. It includes a broad range of interaction potentials and algorithms for electrostatics, hydrodynamics, and coupled particle-field behavior.... -
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GromacsProSuite
Graphical User Interface for Gromacs
This tool is an integrated graphical interface that simplifies molecular dynamics simulations using Gromacs. It provides a structured, tab-based environment to set up, execute, and analyze simulations data without complex command-line operations. The software automates tasks such as topology generation, solvation, ion addition, minimization, equilibration, and production runs while executing GROMACS commands in the background. Built-in monitoring tracks CPU, RAM, and disk usage to ensure... -
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Chemical Trajectory Analyzer
A software package for processing and analyzing chemical trajectories
ChemTraYzer creates reaction models from molecular dynamics simulations. It's available as open software (MIT license). Please find a full description @ https://www.ltt.rwth-aachen.de/cms/LTT/Forschung/Forschung-am-LTT/Model-Based-Fuel-Design/Aktuelle-Projekte/~kqbf/ChemTraYzer/lidx/1 M.Döntgen, M.-D.Przybylski-Freund, L.C.Kröger, W.A.Kopp, A.E.Ismail, K.Leonhard, "Automated Discovery of Reaction Pathways, Rate Constants, and Transition States Using Reactive Molecular Dynamics... -
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QMCF2
Quantum Mechanical Charge Field - Molecular Dynamics
...Interfaces are available for xTB, DFTB+, Gaussian, Turbomole, CRYSTAL, and ASE-based workflows. External programs must be installed separately. Installation: open the Code tab and download or clone the complete repository. On Linux, open a terminal in `qmcf2_installer` and run: `python3 qmcf2_installer.py3` Review the detected compilers, libraries, paths, and warnings, then start the build. The manual is located at `qmcf2_html/qmcf2_doc/manual/qmcf2_manual.pdf`. QMCF2 is research software under active development. Validate calculations on small reference systems before production use. ... -
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LIGGGHTS
This is an academic adaptation of the LIGGGHTS software package
LIGGGHTS-PFM is a Discrete Element Method simulation package maintained for particulate flow modeling. It is based on the LIGGGHTS family and is intended for simulating granular materials, particles, powders, and bulk solids. The project supports Linux installation workflows and is often used alongside CFDEM-style coupling setups. It is useful for researchers and engineers studying particle mechanics, contact behavior, flow through equipment, and industrial bulk handling. The software focuses on particle-level simulation rather than continuum-only descriptions, making it suitable when individual particle contacts and collisions matter. ... -
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CAMPARI
Software for molecular simulations and trajectory analysis
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... -
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the... -
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LIGGGHTS-PUBLIC
Official release of the LIGGGHTS DEM software by DCS Computing
LIGGGHTS-PUBLIC is an open-source Discrete Element Method particle simulation software package. It is used to model granular materials, powders, bulk solids, and industrial particle-flow systems. The project originated from the LIGGGHTS ecosystem and has been used in combination with CFDEM coupling workflows for particle-fluid simulations. It helps users study mechanical contact, particle motion, collision behavior, packing, flow, and equipment-scale granular processes. The software is... -
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rDock
A Fast, OpenSource Program for Docking Ligands to Proteins and N.Acids
...It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies. rDock is mainly written in C++ and accessory scripts and programs are written in C++, perl or python languages. The full rDock software package requires less than 50 MB of hard disk space and it is compilable in all Linux computers. Thanks to its design and implementation, it can be installed on a computation cluster and deployed on an unlimited number of CPUs, allowing HTVS campaigns to be carried out in a matter of days. The rDock program was developed from 1998 to 2006 by the software team at RiboTargets (subsequently Vernalis (R&D) Ltd). ... -
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An open-source software to convert SDF files into TINKER XYZ files (and viceversa) with automatic assignment of MMFF94 atom types, bond types and charges
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This is a general open source Quantum Mechanics/Molecular Mechanics project with academic origin. Its intention is to produce free software tools to study molecular systems through QM/MM, in open collaboration.
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MolTPC
MolTPC provides a solution for fully automatic tautomer enumeration.
Besides all their conformational degrees of freedom, drug-like molecules and natural products often also undergo tautomeric interconversions. Compared to the huge efforts made in experimental investigation of tautomerism, open and free algorithmic solutions for prototropic tautomer generation are surprisingly rare. The few freely available software packages limit their output to a subset of the possible configurational space by sometimes unwanted prior assumptions and complete neglection of... -
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OFR Analysis Tool
For the analysis of output data from the OFR method
The OFR method is a type of steered molecular dynamics method for determining potentials of mean force (PMF) (Phys. Rev. E, 2011, 83: 021114) and local diffusion coefficients, D(z) (Phys. Rev. E, 2012, 86: 036707). OFR-AT is a fast and convenient program for analyzing large output data files from the OFR method, and returns the information necessary to quickly and easily calculate the PMF and D(z) in a spreadsheet. The software is described in detail in the following article: J. Comp.... -
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chemkit is an open source software library for chemistry applications, particularly in the areas of cheminformatics, molecular visualization and molecular modeling.
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OpenCDSurf
Compute CD cavity accessibility
An open-source software aimed at computing cavity accessibility in cyclodextrin derivatives
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