hmacdope
Senior Software Scientist @asapdiscovery @choderalab
ASAP Discovery / @omsfMemorial Sloan Kettering Cancer Center
hmacdope's Stars
gromacs/tng
MDAnalysis/mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
marrink-lab/vermouth-martinize
Describe and apply transformation on molecular structures and topologies
openmm/openmmforcefields
CHARMM and AMBER forcefields for OpenMM (with small molecule support)
leeping/forcebalance
Systematic force field optimization.
ReactionMechanismGenerator/ARC
ARC - Automatic Rate Calculator
jlblancoc/nanoflann
nanoflann: a C++11 header-only library for Nearest Neighbor (NN) search with KD-trees
openpathsampling/openpathsampling
An open source Python framework for transition interface and path sampling calculations.
glotzerlab/freud
Powerful, efficient particle trajectory analysis in scientific Python.
grimme-lab/xtb
Semiempirical Extended Tight-Binding Program Package
plumed/lugano2019
Data for PLUMED tutorial in 2019 in Lugano
SCM-NV/ftl
The Fortran Template Library
SCM-NV/qmflows
This library tackles the construction and efficient execution of computational chemistry workflows
googlecolab/colabtools
Python libraries for Google Colaboratory
aoterodelaroza/nciplot
Non-covalent index plots in molecular systems.
OMaraLab/sushi
Computer set-ups, shell environments, installation notes, etc.
choderalab/openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
tiwarylab/SGOOP
Spectral Gap Optimization of Parameters
lilyminium/compile-settings
Installation notes for computational chemistry packages
ReactionMechanismGenerator/RMG-Py
Python version of the amazing Reaction Mechanism Generator (RMG).
xraypy/xraylarch
Larch: Applications and Python Library for Data Analysis of X-ray Absorption Spectroscopy (XAS, XANES, XAFS, EXAFS), X-ray Fluorescence (XRF) Spectroscopy and Imaging, and more.
dftbplus/dftbplus
DFTB+ general package for performing fast atomistic simulations
MolSSI/EEX
The Energy Expression Exchange for Molecular Dynamics.
clawpack/pyclaw
PyClaw is a Python-based interface to the algorithms of Clawpack and SharpClaw. It also contains the PetClaw package, which adds parallelism through PETSc.
odlgroup/odl
Operator Discretization Library https://odlgroup.github.io/odl/
jeffcomer/DiffusionFusion
Calculate position-dependent diffusivity functions from trajectory data (usually from molecular dynamics). The approach is described in http://doi.org/10.1021/ct300867e . The fractional Smoluchowski model is described in http://doi.org/10.1038/srep35913 .
openmm/openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
mgaitan/fortran_magic
An extension for IPython/Jupyter that helps to use Fortran in your interactive session.
MolSSI/cookiecutter-cms
Python-centric Cookiecutter for Molecular Computational Chemistry Packages
lilyminium/qmtools