compute_fep

Posted on June 30, 2014 by Dan Gezelter

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

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Posted in Molecular Dynamics | Leave a comment

SciDraw

Posted on June 27, 2014 by Dan Gezelter

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 extensive manual fine tuning of the styling of text and graphics.
Find SciDraw at: http://scidraw.nd.edu/

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Posted in Visualization | Leave a comment

MUSCLE

Posted on June 27, 2014 by Dan Gezelter

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 models as defined by the MAPPER project or complex automata as defined in the COAST project.
Find MUSCLE at: http://apps.man.poznan.pl/trac/muscle

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Dendrimer Builder Toolkit (DBT)

Posted on June 27, 2014 by Dan Gezelter

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 and generation of dendrimer.
Find Dendrimer Builder Toolkit (DBT) at: http://www.physics.iisc.ernet.in/~maiti/dbt/home.html

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OpenMM

Posted on June 27, 2014 by Dan Gezelter

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 integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.
Find OpenMM at: https://simtk.org/home/openmm

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Posted in Theoretical and Computational | Leave a comment

DebianScience

Posted on June 27, 2014 by Dan Gezelter

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…)
Find DebianScience at: https://wiki.debian.org/DebianScience

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Posted in Required Reading and Other Sites | Leave a comment

Molecular Dynamics Studio

Posted on June 27, 2014 by Dan Gezelter

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. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications.
Find Molecular Dynamics Studio at: http://sourceforge.net/projects/moleculardynami/

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RunMyCode

Posted on June 27, 2014 by Dan Gezelter

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/

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Voidfinder

Posted on June 27, 2014 by Dan Gezelter

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 comoving cartesian coordinates that the subroutine voidfinder understands.
Find Voidfinder at: http://www.carofoster.com/software

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Posted in Astronomy | Leave a comment

FLOSS for Science

Posted on June 27, 2014 by Dan Gezelter

A site about open source in scientific computing.
Find FLOSS for Science at: http://www.floss4science.com/

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