Search Results for "molecular dynamics simulation fortran"

Showing 88 open source projects for "molecular dynamics simulation fortran"

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  • 1
    Kinetic.jl

    Kinetic.jl

    Universal modeling and simulation of fluid mechanics upon ML

    Kinetic is a computational fluid dynamics toolbox written in Julia. It aims to furnish efficient modeling and simulation methodologies for fluid dynamics, augmented by the power of machine learning. Based on differentiable programming, mechanical and neural network models are fused and solved in a unified framework. Simultaneous 1-3 dimensional numerical simulations can be performed on CPUs and GPUs.
    Downloads: 0 This Week
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  • 2
    Molly.jl

    Molly.jl

    Molecular simulation in Julia

    Much of science can be explained by the movement and interaction of molecules. Molecular dynamics (MD) is a computational technique used to explore these phenomena, from noble gases to biological macromolecules. Molly.jl is a pure Julia package for MD, and for the simulation of physical systems more broadly. The package is described in a talk at Enzyme Conference 2023 and an earlier talk at the JuliaMolSim minisymposium at JuliaCon 2022. Slides are also available for a tutorial in September...
    Downloads: 0 This Week
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  • 3
    VASPKIT
    Basic features: 1. Generate KPOINTS, POTCAR and INCAR for a given POSCAR file; 2. Elastic-constants using stress-strain or energy-strain methods; 3. Equation-of-state fitting; 4. Suggested k-paths for a given crystal structure; 5. Optical adsorption coefficient; 6. Band structure unfolding; 7. Fermi surface; 8. Density-of-states and band-structure; 9. Charge/spin density, Charge density difference; 10. Vacuum level and work function; 11. Wave-function analysis; 12. Molecular...
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    Downloads: 813 This Week
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  • 4
    CAMPARI

    CAMPARI

    Software for molecular simulations and trajectory analysis

    ... 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
    Downloads: 14 This Week
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  • 5
    RINGS "Rigorous Investigation of Networks Generated using Simulations" is a scientific code developed in Fortran90/MPI to analyze the results of molecular dynamics simulations. Its main feature is the analysis of the connectivity using ring statistics.
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    Downloads: 13 This Week
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  • 6
    Atomes

    Atomes

    Analysis, visualization, edition of 3D atomistic models

    Atomes is a Free (Open Source) cross-platform software licensed under the terms of the Affero GPL v3+ license. Atoms is a toolbox developed to analyze, to visualize and to create/edit three-dimensional atomistic models. Atomes also provides an advanced input preparation system for further calculations using well known molecular dynamics codes: - Classical MD : DL-POLY and LAMMPS - ab-initio MD : CPMD and CP2K - QM-MM MD : CPMD and CP2K Atomes is developed by Dr. Sébastien Le Roux...
    Downloads: 41 This Week
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  • 7

    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.
    Downloads: 18 This Week
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  • 8
    loto
    http://loto.sourceforge.net/ hosts 4 projects of free software related to materials science and physics. They are loto, feram, compasses and xtalgrowth.
    Downloads: 3 This Week
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  • 9
    WavePacket (Matlab/Octave)

    WavePacket (Matlab/Octave)

    Dynamics of quantum systems, controlled by external fields

    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, partly also classical or quantum-classical Liouville equations. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate modern...
    Downloads: 4 This Week
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  • 10
    Zgoubi is a ray-tracing code. Since 1972 it pushes charged particles around accelerators and along beam lines, by step-wise resolution of the Lorentz force equation - and their spins by resolution of Thomas-BMT differential equation. Zgoubi is used for charged particle and beam dynamics simulations, and for accelerator and beam line design. It can simulate hadron and lepton beam and polarization dynamics in a large variety of accelerators (storage ring, synchrotron, cyclotron...
    Downloads: 5 This Week
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  • 11
    oxDNA

    oxDNA

    A code primarily aimed at DNA and RNA coarse-grained simulations

    The oxDNA code has been moved to https://github.com/lorenzo-rovigatti/oxDNA, please go there for new releases.
    Downloads: 4 This Week
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  • 12
    ransfoil

    ransfoil

    console to calculate airflow around an airfoil based on RANS approach

    RANSFOIL is a console program to calculate airflow field around an isolated airfoil in low-speed, subsonic, transonic or supersonic regime by numerically solving the Reynolds averaged Navier-Stokes (RANS) equations using mature computational fluid dynamics (CFD) method. As postprocess results, the aerodynamic parameters of the airfoil, e.g., lift coefficient and drag coefficient, can be integrated from the airflow distribution near wall boundary. In addition, the coupling between airflow...
    Downloads: 1 This Week
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  • 13

    MD Log parser

    Standalone application for parsing MD simulation Log files

    The MD Log Parser project focuses on creating a tool designed to parse log files from molecular dynamics (MD) simulations and generate informative graphs. Log files from MD simulations contain crucial details regarding the simulation's progression, energy terms, trajectories, and other pertinent parameters. Extracting and comprehensively analyzing this data manually can be both time-intensive and demanding. Consequently, the MD Log Parser project seeks to automate this procedure, offering...
    Downloads: 0 This Week
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  • 14
    WavePacket (C++/Python)

    WavePacket (C++/Python)

    Time-dependent simulation of open and closed quantum systems

    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 dipole approximation, WavePacket can be used to simulate modern experiments involving ultrashort light pulses in photo-induced physics...
    Downloads: 0 This Week
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  • 15
    PUPIL
    PUPIL (Program for User Package Interface and Linking), is a software environment that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use most...
    Downloads: 0 This Week
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  • 16
    LAMMPS

    LAMMPS

    Large-scale Atomic/Molecular Massively Parallel Simulator

    LAMMPS is a classical molecular dynamics simulator designed for parallel machines. It can model atomic, polymeric, biological, metallic, or mesoscale systems using a variety of force fields and boundary conditions and is easy to modify or extend.
    Downloads: 0 This Week
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  • 17
    Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling.
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    Downloads: 30 This Week
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  • 18
    Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.
    Downloads: 0 This Week
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  • 19

    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...
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    Downloads: 8 This Week
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  • 20
    RMGDFT

    RMGDFT

    Real Space Multigrid based electronic structure code.

    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...
    Downloads: 1 This Week
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  • 21
    APBS

    APBS

    Biomolecular electrostatics software

    This software has moved to http://www.poissonboltzmann.org/.
    Downloads: 0 This Week
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  • 22

    ODFR

    Software for simulation of slow motional EPR spectra in aligned media

    ODFR is intended for simulation of slow-motional EPR spectra for spin-probes (especially nitroxide radicals) in partially oriented samples. The main purpose of the program is the simulation of EPR spectrum angular dependences. Both single- and multiprocessor versions are available. The detailed description of all models and approximations used in the program is contained in the following reference: A.Kh.Vorobiev, A.V.Bogdanov, T.S.Yankova, N.A.Chumakova, “Spin probe determination...
    Downloads: 0 This Week
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  • 23
    MolDynSim

    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...
    Downloads: 0 This Week
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  • 24
    MEMBPLUGIN

    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.
    Downloads: 10 This Week
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  • 25
    AmberAnalysis

    AmberAnalysis

    Command-line tools for analyzing Amber Molecular Dynamics simulations.

    A suite of command-line tools for analyzing chemically relevant features of an Amber Molecular Dynamics simulation. Can detect the position of a planar interface between two substances and plot density relative to that interface for atoms of an arbitrary type, name, charge, or residue. Orientation of three-atom residues (such as water) may be calculated and plotted. Uses parallel processing to detect hydrogen bonds, and can produce a bonding profile. Output files can be displayed as graphs...
    Downloads: 0 This Week
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