OpenScience / Software / Chemistry



molPX: Molecular Projection Explorer

Posted on March 17, 2017 by Dan Gezelter

molPX is an Ipython module that provides, within a Jupyter notebook, interactive molecular visualization of virtually any type of coordinate that a molecular dynamics (MD) trajectory has been projected to. From the more intuitive coordinates, such as distances, contacts, angles … Continue reading →

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Posted in Molecule Viewers and Editors | Leave a comment

IQmol

Posted on July 19, 2016 by Dan Gezelter

IQmol is a easy to use molecular editor and visualization package with the ability to connect to remote servers to run ab initio calculations. Find IQmol at: http://iqmol.org

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Posted in Molecule Viewers and Editors | 1 Comment

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

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 … Continue reading →

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Posted in Polymers | Leave a comment

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 … Continue reading →

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Posted in Theoretical and Computational | 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 … Continue reading →

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Posted in Molecular Dynamics | Leave a comment

Ultrafast Spectroscopy Modelling Toolbox

Posted on June 27, 2014 by Dan Gezelter

User-friendly data analysis for multi-pulse spectroscopy. Matlab-based GUI that helps analyze time-dependent spectroscopic data. Find Ultrafast Spectroscopy Modelling Toolbox at: http://www3.imperial.ac.uk/people/j.vanthor/research/ultrafast_toolbox

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Posted in Spectroscopy | Leave a comment

NWChem

Posted on June 27, 2014 by Dan Gezelter

NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional … Continue reading →

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Posted in Ab Initio Quantum Chemistry | Leave a comment

fOOm-d

Posted on June 20, 2014 by Dan Gezelter

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 Find fOOm-d at: http://foom-d.sourceforge.net/

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MESMER

Posted on June 20, 2014 by Dan Gezelter

MESMER (Master Equation Solver for Multi Energy-well Reactions) models the interaction between collisional energy transfer and chemical reaction for dissociation, isomerisation, association, and non-adiabatic hopping processes. Find MESMER at: http://www.chem.leeds.ac.uk/mesmer.html

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