Open Source Linux Molecular Mechanics Software
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Molecular Mechanics Software for Linux
View 10 business solutionsBrowse free open source Molecular Mechanics software and projects for Linux below. Use the toggles on the left to filter open source Molecular Mechanics software by OS, license, language, programming language, and project status.
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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 initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. http://www.nanoengineer-1.net http://www.ime.unicamp.br/~martinez/packmol/ http://lammps.sandia.gov/ -
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MEMBPLUGIN
MEMBPLUGIN: studying membrane complexity in VMD
MEMBPLUGIN is a membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers. -
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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 Simulations", J. 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. -
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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 stable performance during parallel processing. Beyond simulation execution, it includes advanced trajectory processing and analysis tools such as RMSD, RMSF, SASA, clustering, PCA, hydrogen-bond analysis, Ramachandran plots, and FEL mapping. With integrated visualization and plotting utilities, it offers a unified platform for researchers, educators, and students to perform complete MD workflows efficiently and reproducibly. Our Goal is to bring MD simulations to every biologist's toolkit. -
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rDock
A Fast, OpenSource Program for Docking Ligands to Proteins and N.Acids
rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic 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). In 2006, the software was licensed to the University of York for maintenance and distribution. In 2012, Vernalis and the University of York agreed to release the program as Open Source software. -
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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 analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion. CAMPARI offers the user a very high level of control over all implemented features. For more information and features, please refer to the project's homepage at http://campari.sourceforge.net/V5 -
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MDcons(Molecular Dynamics consensus)
Interpretation of Biomolecular MD simulations
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. -
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Renumber Gromacs Top & Gro Files
Renumber Gromacs .top and .gro files
Renumber Gromacs .top and .gro files after removing atoms (e.g. hydrogens) for input into grompp -
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pyMDMix
Molecular dynamics with aqueous-organic solvent mixtures
This python package aims to help people set up and analyze molecular dynamics simulations in aqueous-organic solvent mixtures. See D. Alvarez-Garcia et al. Journal of Medicinal Chemistry, 2014. -
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APL@Voro
APL@Voro a tool for model bilayer simulation analysis.
APL@Voro is a program designed to aid in the analysis of lipid bilayer simulations carried out by gromacs. It calculates the area per lipid and the membrane thickness even for mixed bilayers. Colored Voronoi diagrams and different types of plots are presented in an interactive environment. -
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We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.
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AutoMap
AutoMap is a tool for structural biology and drug design.
AutoMap takes a series of poses obtained from molecular docking and applies the site, epitope and conformational mapping techniques to the poses to select likely ligand binding modes. -
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ESTReMo
An evolutionary simulator of transcription regulatory networks
ESTReMo is a genetic algorithm-based simulator to explore the evolution of transcription factors and their binding motifs on realistic genomic backgrounds. -
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Iphigenie
A fast and versatile molecular dynamics program
The molecular mechanics (MM) program Iphigenie provides a broad range of molecular dynamics (MD) methods and technologies, including polarizable force fields (PMM), the HADES reaction field, and QM/(P)MM hybrid simulations. -
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MIPGen
Simple Molecular Interaction Potential Generator in Python
Molecular Interaction Potential Generator MIPGEN is a python program that will calculate Molecular Interaction Potential grids over a given molecule, that could be either a protein or a small organic compound (drug). The output will be a series of grids with DX format (*.dx) that the user will be able to visualize using any Molecular visualization program like VMD, PyMol, Chimera... For more information on dependencies and usage, please read the Documentation. Users are welcome to post any bug or request under BUGS & REQUESTS menu. (sourceforge account will be needed). -
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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 ring-chain tautomerism. MolTPC provides an adjustable and fully automatic approach for this problem. The original publication can be found on http://onlinelibrary.wiley.com/doi/10.1002/jcc.23397/full. -
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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. Phys., 231(11): 4355-4364. -
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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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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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ParamIT
a Toolset for Molecular Mechanical Force Field Parameterization
ParamIT is a toolkit aiding the development of molecular mechanical force field parameterization of small, drag like, molecules within CHARMM general force field (CGenFF) protocol. The developed toolkit helps the researchers in following ways: 1) automating the creation of multiple input files for quantum and molecular mechanics programs, 2) automating the output analysis and 3) substitute the use of full MM programs with a faster specialized one. The developed tools include: 1) generator 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. -
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PyBrella
Python script to automate umbrella sampling with AMBER
PyBrella is a script designed to automate the umbrella sampling process, using the AMBER molecular dynamics package. -
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QDC (quick direct-method controlled) is an optimized exact implementation of the Gillespie's direct-method. It is designed for biochemical simulations when there is the need of dynamic parameters whose values can change during the simulation.
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QTASEP
Visualization application for various TASEP, ASEP and SSEP models.
Visualization of TASEP, ASEP, SSEP models with various update rules based on Zarja simulation library using QT GUI library. -
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SPiM2Eclipse
Eclipse plugin for Stochastic Pi Machine
Stochastic Pi Machine (SPiM), created by Microsoft, is a programming language for modeling biological processes. Two tools are available from Microsoft for simulation. A web application Visual SPiM, and a destkop application SPiM Player. Both simulation tools require to be run on a Windows platform. Fortunately Microsoft has also released a command line version for Linux and Mac OS based on OCAML however this version will only output a CSV file for the simulation results. SPiM2Eclipse provides a bridge for those running SPiM from the command-line by allowing simulations to be completed by a single click, displaying an embedded plot of the results. Features: -As an Eclipse plugin you have all of the powerful features of Eclipse available to you. -Syntax color highlighting -One-click simulation with plotting For more information on SPiM see the offical project website at: http://research.microsoft.com/en-us/projects/spim/ -
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TrajLab
MATLAB based programs for trajectory simulations of molecules
TrajLab (which stands for TRAJectory LABoratory) consists of two sets of MATLAB program packages. While subproject MolDynSim deals with generation of molecular trajectories (and other aspects of molecular simulation), subproject MetaStable is dedicated to the analysis of molecular trajectories by detecting metastable conformations (as well as other analysis techniques). Note that each of the two sub-projects has its own SVN repository, wiki, tracker, etc: Probably TrajLab is the first attempt for a general purpose molecular simulation package in MATLAB. While the authors are aware that many other highly specialized and highly optimized program packages for the same purpose exist (e. g. AMBER, GROMACS, NAMD, etc.), the MATLAB environment offers easy access to manipulating the codes, testing novel algorithms, non-standard force fields and performing all kinds of numerical experiments. To be used mainly in teaching!
