Search Results for "gromacs"
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Showing 28 open source projects for "gromacs"
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GrOWin
Gromacs on Windows
We welcome you to explore the cutting-edge capabilities of Growin, the innovative project as it breaks platform barriers by introducing a Windows version of GROMACS. Growin goes beyond conventional boundaries, delivering a seamless experience on Windows operating systems, ensuring accessibility to a broader user base. 1. Cross-Platform Compatibility: Growin extends the reach of GROMACS by introducing a dedicated Windows version, allowing users on this platform to harness the power of GROMACS... -
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ERmod
Approximate solvation free energy calculator
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. -
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CheUP
Gromacs Topology Builder - OPLS AA Based. Support many charge model
CheUP is a program to create GROMACS topology for molecular dynamic simulation seamlessly with less learning curve based on OPLS-AA Force Field. It is designed for newcomer in molecular dynamic as well as for expert in this field. The user has choice to use several types of charge models and quantum software or using OPLS database to generate the topology. Moreover, user can use own parameter as well as original OPLS parameter. Finally, user also can add and edit the topology within... -
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silico
Libraries and scripts for molecular modelling written in Perl
A perl molecular toolkit designed to assist in general molecular modelling activities. Silico provides file format conversion, molecular manipulation and analysis and a simple way to write wrapper scripts around other preexisting software packages. -
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ForceGen
Derives force constants from Gaussian QM for Gromacs MD
Please cite: ForceGen: atomic covalent bond constant derivation for Gromacs. Nash A, Collier T, Birch HL, de Leeuw NH. Journal of Molecular Modeling (2018), (24)5. DOI: 10.1007/s00894-017-3530-6 Instruction video: https://youtu.be/fQVXv8Ge_tg This Java executable jar derives second order bond force constants for bond stretch and bond angle from quantum mechanical Gaussian calculations. The calculations are compatible with the Amber force field family or any force field derived from... -
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MolDynSim
TrajLab subproject: Molecular dynamics simulations in MATLAB
This is a subproject of TrajLab which is probably 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 research... -
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MetaStable
TrajLab subproject: Metastability analysis of molecular conformations
This is a subproject of TrajLab which is probably 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 research... -
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VITAMINS
Visual and Insitu Analytics for Molecular Interactive Simulation
A framework to support the high performance analysis and visualisation of molecular dynamics trajectories directly acquired in-situ while the simulation is running, or read from files. Vitamins relies on the FlowVR software and comes with binding with Gromacs. Vitamins (Visual and In Situ Analytics for Molecular Interactive Simulation) is an open source framework for the analysis and visualisation of large molecular dynamics trajectories directly acquired in-situ while the simulation... -
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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...
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ProtPOS
Prediction of PROTtein Preferred Orientation on a Surface
... simulations. ProtPOS is implemented in Python, making use of the PyMOL library for generating protein conformations and calling GROMACS externally to calculate protein-surface interaction energies. https://cbbio.online/software/protpos/ -
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DMap Sampling (GROMACS)
Modified version of GROMACS needed for Diffusion Map Sampling
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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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eSBMTools
python tools for enhanced native structure-based modeling
eSBMTools: python tools that assist the setup and evaluation of native structure-based simulations of proteins and nucleic acids, both at the Cα and all-atom level. The tools interface with GROMACS and support its standard output formats. Information from other sources like bioinformatics or experimental data can be added to the standard native structure-based model (SBM). Publication to be cited: Benjamin Lutz, Claude Sinner, Geertje Heuermann, Abhinav Verma, and Alexander Schug. eSBMTools... -
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Bio.B-Gen
Initial system (box) generator for biological molecular simulations
"Bio.B-Gen" is a command line tool to generate initial systems for biological molecular simulations. "Bio.B-Gen" was mainly designed to be used with the GROMACS molecular dynamics simulation package (http://www.gromacs.org). "Bio.B-Gen" depends on the GROMACS topology and force field information (.top and .itp data files) during the generation stage. "Bio.B-Gen" adds specified number of copies of a molecule to an existing configuration to a specified spacial domain inside the system... -
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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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GROsolEv4.5
Calculates pairwise energies from Gromacs simulations.
Calculates intermolecular energies for solvent-solvent interactions, for solvent confined to environments a few angstroms in diameter. Algorithm uses a spherical approximation to describe the confined environments geometry. -
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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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Grid3D Toolbox
3D grid toolbox for analysis of molecular simulations
"Grid3D Toolbox" is a set of command line tools for visualization and analysis of the results of molecular simulations based on 3-dimensional density maps (grids). Currently, the tools only work with the simulation trajectories generated by the GROMACS simulation package (http://www.gromacs.org/). The generated density maps are saved in the Grid3D native .g3d format and can be visualized using a third party data visualization software. A converter from the .g3d format to .vti, an XML based... -
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Gromacs
Gromacs for Windows
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. -
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DDPT
A Comprehensive Toolbox for the Analysis of Protein Motion
Toolbox allowing calculation of elastic network models and principle component analysis. It allows the analysis of pdb files or trajectories taken from; Gromacs, Amber, and DL POLY. As well as calculation of the normal modes it also allows comparison of the modes with experimental protein motion, variation of modes with mutation or ligand binding, and calculation of molecular dynamic entropies. -
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NaRIBaS
Unix-based preparation and analysis toolbox for molecular simulations
Unix-based preparation and analysis toolbox for Nanomaterials and Room Temperature Ionic Liquids in Bulk and Slab using bash scripts, Gromacs tools and Matlab functions. NaRIBaS provides a framework that decouples user input parameter and terminal based command lines. NaRIBaS does not replace a simulation software and specific analysis tools like Gromacs, but it allows iterative repetition of tasks while changing specific input parameter. The toolbox is to be understood as a scripting... -
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TrajLab
MATLAB based programs for trajectory simulations of molecules
... 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! -
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This project contains a custom version of the GROMACS molecular dynamics software package that helps users to choose parameters for the PME electrostatics model which produce a known error in the PME approximation for minimal computational cost.
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jSim for Gromacs is a Graphical User Interface for the Molecular Dynamics Package Gromacs. It has a project style interface to organize your md simulations. It is also possible to start md simulations on remote computers with ssh.
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