Search Results for "molecular"
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Showing 101 open source projects for "molecular"
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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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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 . -
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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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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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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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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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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...
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VASPMO
Visualization of wavefunctions calculated by VASP (New release: v0.41)
VASPMO aims at visualizing wavefunctions (or molecular orbitals) from VASP calculations. It reads VASP's output files PROCAR and CONTCAR, and exports an *.out file in Gaussian's output format, which can be visualized by many popular visualization tools, such as JMol, Molekel, Chemcraft, Gabedit and Molden, etc. These tools can further generate *.cube files, which can be visualized by an even wider range of softwares. -
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Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/. -
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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. ... -
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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. -
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PF_HP
Prediction of proteinfolding in 2D HP model
Even in the simplified two dimensional HP-model (hydrophob/polar) the prediction of proteinfolding is NP complete. We implement a brute force algorithm with serial and parallel execution to solve short inputs of HP sequences (0-1 bitstrings). Selbst im vereinfachten zweidimensionalen HP-Modell (hydrophob/polar) ist die Proteinfaltung bereits NP-vollständig. Hier implementieren wir einen brute-force Algorithmus zur Lösung kurzer Eingabesequenzen (0-1-Bitstrings) für die... -
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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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RElt
calculates overlap, kinetic integrals for numerical atomic orbitals.
The efficient algorithm calculating the overlap and the kinetic integrals for the numerical atomic orbitals is implemented. The described algorithm exploits the properties of the prolate spheroidal coordinates. The overlap and the kinetic integrals in R^3 are reduced to the integrals over the rectangular domain in R^2, what substantially reduces the complexity of the problem. We prove that the integrand over the rectangular domain is continuous and does not have any slope singularities. For... -
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diauxic growth model ensemble
An ensemble of models showing diauxic growth behavior
An ensemble of mathematical model is presented that all show diauxic growth behaviour of a bacterial culture. Carbon catabolite repression (CCR) is the main mechanism controlling carbohydrate uptake in bacteria, and therefore also controlling whether or not different carbon sources are metabolized in parallel or sequentially. Although described as a paradigm of the regulation of bacterial metabolism, the underlying mechanisms remain controversial. The models in the ensemble can... -
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Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS
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RAtom
solves nonlinear Kohn-Sham equation for the neutral atom.
...Mater. Sci. Eng. vol. 17, 045001 (2009) 2. Z. Romanowski, "Application of h-adaptive, high order finite element method to solve radial Schrödinger equation", Molecular Physics, vol. 107, pp. 1339-1348 (2009). Further questions: romz@wp.pl -
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Molecular Simulation Grid
Provides high performance computing power and state of the art tools
MoSGrid focuses on the configuration and provision of Grid services for molecular simulations and annotation of the results with metadata and their provision for data mining and knowledge generation. It is based on Liferay technology togethe with gUSE. -
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RSchr-5
Solves one-electron Schrödinger equation, with SLEPc and PETSc
RSchr-5 calculates the smallest eigenvalues of the one-electron Schrödinger equation. The solved problem is defined on the finite domain, which is a box. The problem is solved with the zero Dirichlet boundary conditions. The implemented algorithm uses Finite Element Method with B-splines as basis functions. Disctretization leads to generalized eigenvalue problem. Program RSchr-5 solves the generalized eigenvalue problem by algorithms implemented in SLEPc amd PETSc libraries. It uses... -
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Virtual Cell
Former home of the Virtual Cell platform (VCell), see http://vcell.org
This project and all source code has moved to GitHub, see https://github.com/virtualcell -
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TUBE
Generating structures of nanotubes and some fullerenes
A Windows software for generating structures of nanotubes and some fullerenes. You can generate any kind of nanotubes (n,m) with chirality indices n and m ranging from 0 to 60, and the number of repetitive unit cells up to 50. You can also generate some typical fullerene cages from C20 up to C320. -
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PDBManip
PDBManip is a free program for editing PDB (Protein Data Bank) Files
PDBManip is a free program for editing and manipulating PDB (Protein Data Bank) files. It has a graphical user interface and it is provided as an executable file for running on Windows® operating systems. There is a bunch of free programs on the internet for the same purpose. What discriminate between PDBManip and those programs is that PDBManip uses AngelScript language which is very similar to C/C++ language, to write scripts to do our editing tasks. I know that the text-manipulation... -
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LOOS
Analyze molecular simulation data
LOOS is a light-weight object oriented software library for creating new tools for analyzing molecular simulation data, written in C++. The main design goal is to allow casual programmers to easily implement new analysis methods. THIS PAGE IS NO LONGER UPDATED. Please see https://github.com/GrossfieldLab/loos for all recent developments
