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Author Archives: Dan Gezelter
LabJ
LabJ (a.k.a Electronic Laboratory Notebook, ELN, Laboratory Journal) assists in planning chemical reactions and stores chemical information. Open Source, but it requires ISIS Desktop package from MSI. Find LabJ at: http://www.karolgrela.eu/labj/
Posted in Chemistry
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GPeriodic
Posted in Periodic Tables
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TINKER
The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for polypeptides. Find TINKER at: http://dasher.wustl.edu/tinker/
Posted in Molecular Dynamics
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MathML in Mozilla
Project to add Math Markup language to our last best hope at an open source browser. Find MathML in Mozilla at: http://www.mozilla.org/projects/mathml/
Posted in Tools
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ROOT
An Object Oriented Framework For Large Scale Data Analysis (used primarily in the high-energy and nuclear physics community). Find ROOT at: http://root.cern.ch/
Posted in Physics
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Netlib
An incredibly useful set of libraries for numerical computation. Find Netlib at: http://www.netlib.org
Posted in Mathematics
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NIMROD
a code suitable for the study of long-wavelength, low-frequency, nonlinear phenomena in realistic toroidal geometry, including Tokamaks, Spheromaks, Reversed Field Pinches, and Field-Reversed Configurations Find NIMROD at: http://www.nimrodteam.org/
Posted in Plasma
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Guppi
Guppi is an interactive data analysis application. Guppi is meant to be both powerful and user-friendly. Guppi is not a clone of any existing system, but it is meant to be a free replacement for proprietary tools like Systat, IDL … Continue reading
Posted in 2D Plotting
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BallRoom
a tool to draw large ensembles of atoms Find BallRoom at: http://www.fisica.uniud.it/~ercolessi/ballroom.html
Posted in Molecule Viewers and Editors
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MOSCITO
Moscito is designed for condensed phase and gas phase MD simulations of molecular aggregates. Standard molecular mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS can be employed. Simulations can be carried out in different ensembles such as NVE, NVT … Continue reading
Posted in Molecular Dynamics
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