Search Results for "molecular dynamics" - Page 3
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Showing 105 open source projects for "molecular dynamics"
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sphrheo
SPH add-on to LAMMPS for the rheology of Non-Newtonian liquids
This package comprises a set of add-ons to the popular LAMMPS molecular dynamics software to study the rheology of Non-Newtonian liquids with moving boundaries. Licensed under the GPL, this software is free to use and reproduce under the same terms. It is simple to install and extend. At the current stage, it provides libraries for strain-rate dependent viscosity, a dynamic stress model (Rolie-Poly), and the inclusion of colloidal particles in a viscoelastic solvent. -
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piv_clustering
structural clustering of atomic trajectories based on PIV
This program allows to perform a structural cluster analysis of atomic trajectories obtained, e.g., from molecular dynamics simulations. At variance with other approaches, it is possible to analyse also processes in solution, e.g., chemical reactions in liquid water, since the distance metric is based on a Permutation Invariant Vector (PIV) that is symmetric under exchange of identical atoms or molecules, including on the same footing both solute and solvent degrees of freedom. The approach... -
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allink
Software for data analysis, image processing, simulations, solver.
Collection of utilities based on two basics classes: Matematica and VarData. Matematica) performs math operations on vectors and matrices for smoothing, interpolation, convolution, image processing... VarData) manipulate a structure of points connected by links. Addraw) openGL engine. ElPoly) analyze mechanical properties of polymer and membrane like structures. Addyn) perform molecular dynamics and Monte Carlo simulations and has a solver for 4th oder PDE. Avvis) perform all... -
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fOOm-d (framework for Object Oriented molecular dynamics) is a molecular dynamics framework with an emphasis on methods that require coupling of separate trajectories - e.g., EVB methods and a range of classical-trajectory guided quantum dynamics methods
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GridMD is the C++ class library intended to help the developers to quickly build the molecular dynamics or Monte-Carlo simulation programs and to run it in the distributed environment.
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The Python Unified Membrane Analysis Toolkit is a suite of python tools for analyzing molecular dynamics simulations of membranes.
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ASyncRE-BigJob
Asynchronous Replica Exchange with BigJob
A distributed replica exchange molecular dynamics framework written in Python built on top of BigJob (https://github.com/saga-project/BigJob/wiki). The software is extensible to any molecular dynamics engines. Modules for AMBER and IMPACT are included. Download: https://sourceforge.net/projects/asyncrebigjob/files/latest/download See README for installation instructions. See documentation in doc/ subdirectory. Git access: git clone https://github.com/saga-project/asyncre-bigjob -
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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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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... -
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X3DBio2
A visual analysis tool for biomolecular structure comparison
A major problem in structural biology is the recognition of differences and similarities between related three dimensional (3D) protein structures. X3DBio2 is a visual analysis tool for 3D biomolecular structure comparison that allows for a clear comparison between similar structures from various species, for elucidation of structural effects of mutations, and for assessment of snapshots from molecular dynamics trajectories. X3DBio2 is the second milestone in a larger project currently... -
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FES-TOOLS
A set of Tools for analysing PLUMED FES data
PLUMED is a set of pathches that permits to perform MetaDynamics simulations using the most popular Molecular Dynamics software. FES-TOOLS is a tool of analysis of the PLUMED output files. -
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Protein Stability
VIRTUAL QUANTIFICATION OF PROTEIN STABILITY
Protein stability, the most important aspect of molecular dynamics and simulations, requires sophisticated instrumentations of molecular biology to analyze its kinetic and thermodynamic background. Sequence- and structure-based programs on protein stability exist which relies only on single point mutations and sequence optimality. The energy distribution conferred by each amino acid essentially paves way for understanding protein stability. To the best of our knowledge, Protein Stability... -
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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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several versions of molecular dynamics code for hcpp course work in Msc in High performance computing university of edinburgh
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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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ODD is a tool for optimal domain decomposition of atomic structure guided by the given molecular dynamics data.
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birgHPC is a Linux Live CD distribution based on PelicanHPC and Debian Live. birgHPC features automated cluster configuration on PCs in the same network specifically for bioinformatics and molecular dynamics. If you are looking for CUDA support, try birgHPCC (https://sourceforge.net/projects/birghpcc/) If you use birgHPC in your work, please cite us: Teong Han Chew, Kwee Hong Joyce-Tan, Farizuwana Akma and Mohd Shahir Shamsir. birgHPC: creating instant computing clusters...
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BioSpring is a molecular simulation software based on a spring network model, including non-bonded interactions, especially designed for Interactive Molecular Dynamics. It incorporates MyPal for locating ion binding sites and IMPALA for interactive placement of membrane proteins in a membrane environment.
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Perform molecular dynamics clustering.
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Molecular Dynamics clustering using several algorithms.