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Author Archives: Dan Gezelter
compute_fep
Free energy perturbation for LAMMPS, with soft-core pair potentials. Uses FEP, Thermodynamic Integration (TI), Mezei FDTI, and Bennet Acceptance Ratio methods. It can be used for alchemical transformations of pair potentials or charges in selected atoms. Find compute_fep at: https://github.com/agiliopadua/compute_fep
Posted in Molecular Dynamics
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SciDraw
SciDraw is a system for preparing publication-quality scientific figures with Mathematica. SciDraw provides both a framework for structuring figures and tools for generating their content. SciDraw helps with generating figures involving mathematical plots, data plots, and diagrams. The package allows … Continue reading
Posted in Visualization
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MUSCLE
MUSCLE 2 – The Multiscale Coupling Library and Environment is a portable framework to do multiscale modeling and simulation on distributed computing resources. The generic coupling mechanism of MUSCLE is suitable for many types of multiscale applications, notably for multiscale … Continue reading
Posted in Data Communication
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Dendrimer Builder Toolkit (DBT)
DBT can be used to build polymers (linear or hyperbranched) for use in AMBER depending upon multiplicity of joining residues. DBT sequences and calculates the number of residues required for building dendrimer (or polymer), which further depends on core multiplicity … Continue reading
Posted in Polymers
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OpenMM
OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It provides a combination of extreme flexibility (through custom forces and … Continue reading
Posted in Theoretical and Computational
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DebianScience
Provides researchers and scientists a better experience when using Debian. Classifies, packages and distributes free software useful to science and research. Supports quality efforts around free scientific software. Manages these efforts when dealing with various library implementations (MPI, BLAS, LAPACK…) … Continue reading
Molecular Dynamics Studio
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 … Continue reading
Posted in Molecular Dynamics
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RunMyCode
RunMyCode enables scientists to openly share the code and data that underlie their research publications This service is based on the innovative concept of a companion website associated with a scientific publication. Find RunMyCode at: http://www.runmycode.org/
Voidfinder
Finds and quantifies empty space. Voidfinder is a Fortran subroutine that takes the position of galaxies in cartesian coordinates. Some subroutines used in the body of SDSSvoidfinder (the main program) are used to convert the ra, dec and redshift into … Continue reading
Posted in Astronomy
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FLOSS for Science
A site about open source in scientific computing. Find FLOSS for Science at: http://www.floss4science.com/