Search Results for "molecular simulation"
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Showing 163 open source projects for "molecular simulation"
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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. -
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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. -
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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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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. -
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LAMMPS
Public development project of the LAMMPS MD software package
...It supports many interaction models, including pair potentials, many-body potentials, reactive force fields, bonded interactions, long-range electrostatics, and user-extendable packages. LAMMPS is script-driven, so users can define simulation geometry, force fields, integration methods, output, and analysis behavior through input files. Its main value is combining broad scientific flexibility with scalable parallel performance for complex molecular and mesoscale simulations. -
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BioNeMo
BioNeMo Framework: For building and adapting AI models
BioNeMo is an AI-powered framework developed by NVIDIA for protein and molecular generation using deep learning models. It provides researchers and developers with tools to design, analyze, and optimize biological molecules, aiding in drug discovery and synthetic biology applications. -
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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. -
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QMCF2
Quantum Mechanical Charge Field - Molecular Dynamics
QMCF2 is a molecular-simulation package for molecular dynamics, Monte Carlo, geometry optimization, molecular mechanics, and combined quantum-mechanical/molecular-mechanical calculations. The source includes force-field, electrostatics, constraints, thermostats, pressure control, water models, QMCF/QM-MM, external-QM interfaces, conversion tools, and analysis utilities. -
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NAMD-Automator
A GUI to automate Workflow for setting up and run NAMD simulations
Welcome to NAMD-Automator, a user-friendly graphical interface designed to simplify the process of Molecular Dynamics (MD) Simulation, by creating configuration files, and automate the simulation with simple form-based tabs. NAMD is one of the widely used software for running these simulations, known for its scalability, speed and efficiency with large molecular systems. However, setting up a typical simulation in NAMD usually requires crafting configuration file for each stage of a Conventional MD Simulation (CMD), such as Minimization, Heating, Equilibration and Production. ... -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Published in Wiley, Journal of Computational Chemistry . Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us -... -
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ERmod
Approximate solvation free energy calculator
...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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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. -
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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. -
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ChemCalc
Easily set up simulations or estimate needed amounts
A program that converts between the various categories of amounts: - Absolute amount (number of moles, mass, volume) - Relative amount (mole fraction, mass fraction, volume fraction) - Solute concentration (molarity, molality, mass concentration, specific volume) Assumes incompressibility for simplicity. Requires molar mass and density for each component. Very generic utility. Examples of use: - Setting up a simulation by obtaining the mole fractions of each molecular entity - Anticipating the amounts of raw materials required to carry out a multi-step preparation for a chemical reaction -
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http://loto.sourceforge.net/ hosts 4 projects of free software related to materials science and physics. They are loto, feram, compasses and xtalgrowth.
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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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Eleana
Program for the analysis of spectroscopic data, in particular EPR(ESR)
Eleana is a program for manipulating, modifying and analyzing various spectroscopic data, in particular electron paramagnetic resonance spectra. It allows you to import data from Bruker spectrometers such as Elexsys or EMX and data from any ASCII file or imported from the clipboard. The program is under constant development, but already has many functions implemented for spectral analysis. Some of the basic functions include: baseline corrections, filtering, spectral clipping, integration /... -
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WavePacket (C++/Python)
Time-dependent simulation of open and closed quantum systems
Note: This package has been superseded by a Python-only package. See https://github.com/ulflor/wavepacket for the follow-up project. 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... -
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Optimizer_sovkov
Constructing and optimizing general mathematical and physical models
...Elementary model blocks can be collected in libraries, and we have already written many such library programs. Many of these programs are already available along with the main package. Currently, the main focus of these is computational quantum mechanics, analysis and simulation of molecular spectra, and general-purpose approximants. The package provides the most reliable modern strategies for linear and non-linear model optimization, regularization, and hypothesis tests. Parallel computing is supported. -
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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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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... -
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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... -
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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 researchers a user-friendly tool to efficiently extract valuable insights from MD simulation log files. -
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almost - all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.
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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...
