JOSS Papers: Molecular Dynamics

Published Papers

published Published about 2 years ago

HOOMD-TF: GPU-Accelerated, Online Machine Learning in the HOOMD-blue Molecular Dynamics Engine

C++ Cuda Python

@RainierBarrett

10.21105/joss.02367

published Published about 2 years ago

taurenmd: A command-line interface for analysis of Molecular Dynamics simulations.

Python

@joaomcteixeira

10.21105/joss.02175

published Published over 2 years ago

pygen-structures: A Python package to generate 3D molecular structures for simulations using the CHARMM forcefield

Python

10.21105/joss.02157

published Published over 2 years ago

BioSimSpace: An interoperable Python framework for biomolecular simulation

Python Jupyter Notebook

10.21105/joss.01831

published Published almost 3 years ago

PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python

C++ Python

10.21105/joss.01773

published Published almost 3 years ago

CSaransh : Software Suite to Study Molecular Dynamics Simulations of Collision Cascades

C++ Python JavaScript

10.21105/joss.01461

published Published almost 3 years ago

Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD

Tcl

10.21105/joss.01698

published Published over 3 years ago

idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments

Python Jupyter Notebook

10.21105/joss.01007

published Published almost 4 years ago

tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations

Python

10.21105/joss.00877

published Published over 4 years ago

MDEntropy: Information-Theoretic Analyses for Molecular Dynamics

Python Batchfile

10.21105/joss.00427

Displaying papers 11 - 20 of 21 in total

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ISSN 2475-9066