GitPlanet

Cheap and reliable Node.js hosting starts at $3/month, and $1/month static HTML hosting

Created with love in Canada, visit hostnodejs.com today

Feel like to post an Ad? Learn Details
All Projects → aqlaboratory → Pnerf

aqlaboratory / Pnerf

Licence: mit

Programming Languages

python
139335 projects - #7 most used programming language

Labels

machine-learningmolecular-dynamics

Projects that are alternatives of or similar to Pnerf

perses
Experiments with expanded ensembles to explore chemical space
Stars: ✭ 99 (+253.57%)
Mutual labels:  molecular-dynamics
ls1-mardyn
ls1-MarDyn is a massively parallel Molecular Dynamics (MD) code for large systems. Its main target is the simulation of thermodynamics and nanofluidics. ls1-MarDyn is designed with a focus on performance and easy extensibility.
Stars: ✭ 17 (-39.29%)
Mutual labels:  molecular-dynamics
Mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
Stars: ✭ 589 (+2003.57%)
Mutual labels:  molecular-dynamics
tinker9
Tinker9: Next Generation of Tinker with GPU Support
Stars: ✭ 31 (+10.71%)
Mutual labels:  molecular-dynamics
pyemma tutorials
How to analyze molecular dynamics data with PyEMMA
Stars: ✭ 49 (+75%)
Mutual labels:  molecular-dynamics
hoomd-examples
HOOMD-blue example scripts.
Stars: ✭ 15 (-46.43%)
Mutual labels:  molecular-dynamics
Aboria
Enables computations over a set of particles in N-dimensional space
Stars: ✭ 83 (+196.43%)
Mutual labels:  molecular-dynamics
Hoomd Tf
A plugin that allows the use of Tensorflow in Hoomd-Blue for GPU-accelerated ML+MD
Stars: ✭ 25 (-10.71%)
Mutual labels:  molecular-dynamics
grand
A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.
Stars: ✭ 23 (-17.86%)
Mutual labels:  molecular-dynamics
Awesome Python Chemistry
A curated list of Python packages related to chemistry
Stars: ✭ 410 (+1364.29%)
Mutual labels:  molecular-dynamics
pytraj
Python interface of cpptraj
Stars: ✭ 106 (+278.57%)
Mutual labels:  molecular-dynamics
tinker
Tinker: Software Tools for Molecular Design
Stars: ✭ 79 (+182.14%)
Mutual labels:  molecular-dynamics
Schnetpack
SchNetPack - Deep Neural Networks for Atomistic Systems
Stars: ✭ 296 (+957.14%)
Mutual labels:  molecular-dynamics
AdaptivePELE
AdaptivePELE is a Python package aimed at enhancing the sampling of molecular simulations
Stars: ✭ 14 (-50%)
Mutual labels:  molecular-dynamics
Openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
Stars: ✭ 791 (+2725%)
Mutual labels:  molecular-dynamics
uf3
UF3: a python library for generating ultra-fast interatomic potentials
Stars: ✭ 19 (-32.14%)
Mutual labels:  molecular-dynamics
isicle
In silico chemical library engine for high-accuracy chemical property prediction
Stars: ✭ 31 (+10.71%)
Mutual labels:  molecular-dynamics
Uammd
A CUDA project for Molecular Dynamics, Brownian Dynamics, Hydrodynamics... intended to simulate a very generic system constructing a simulation with modules.
Stars: ✭ 11 (-60.71%)
Mutual labels:  molecular-dynamics
Pydhamed
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
Stars: ✭ 17 (-39.29%)
Mutual labels:  molecular-dynamics
Mdtraj
An open library for the analysis of molecular dynamics trajectories
Stars: ✭ 317 (+1032.14%)
Mutual labels:  molecular-dynamics
View All Similar Projects ➔

pNeRF: Parallelized Natural Extension Reference Frame

pNeRF is a parallelized extension of the widely used NeRF method for converting the parameterization of polymers, typically proteins, from internal (bond lengths, angles, and torsions) to Cartesian coordinates. pNeRF is parallelized even for individual polymers, achieving much higher utilization of modern CPUs and GPUs, and is suitable for use in machine learning applications in which gradients are backpropagated through the NeRF equations.

This is a TensorFlow implementation of pNeRF. Using this implementation we observe speed ups of up to 13x on CPUs (Xeon E5-2643 v4) and GPUs (Titan Xp):

Color intensity corresponds to fold speed up.

PyTorch Implementation

A PyTorch implementation of pNeRF has been developed by @FelixOpolka and is available here.

Citation

Please cite this paper in the Journal of Computational Chemistry.

Funding

This work was supported by NIGMS grant P50GM107618.

Note that the project description data, including the texts, logos, images, and/or trademarks, for each open source project belongs to its rightful owner. If you wish to add or remove any projects, please contact us at [email protected].