byun-jinyoung Goto Github PK

nnpops

High-performance operations for neural network potentials

openbpmd

OpenBPMD for MD_VS

openff-toolkit

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

openmm-atmmetaforce-plugin

An OpenMM plugin that implements the Alchemical Transfer Potential

openmm-cookbook

Proof-of-concept for the OpenMM Cookbook

openmm-pulling

Pulling Simulation and Smoothing

openmm-torch

OpenMM plugin to define forces with neural networks

openmm-tutorial-msbs

OpenMM tutorial for the MSBS course

openmm-tutorials

Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM

openmm_ramd

Allows one to run RAMD simulations in OpenMM

openmmenergycomparisons

Comparisons of energies and forces between OpenMM and other packages

ownmy-software-installation-guide

Trial and errors of software installation

paddlehelix

Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

painn-jax

PaiNN in jax

papers

Material from papers from KULL centre

papers_for_protein_design_using_dl

List of papers about Proteins Design using Deep Learning

paprika

Advanced toolkit for binding free energy calculations

parafold

Open source code for AlphaFold.

pdb-sublime3-plugin

Sublime 3 plugin for the PDB files (Atomic Coordinate Entry Format)

peg

performer-pytorch

An implementation of Performer, a linear attention-based transformer, in Pytorch

perses

Experiments with expanded ensembles to explore chemical space

pesto

pf-gnn_pli

pigvae

pka-ani

Accurate prediction of protein pKa with representation learning

plumed-westpa

plumed-with-amber-and-gromacs

In this pdf file i have wrote down the important steps for installing of plumed , gromacs nad amber and patching the PLUMED with other MD engines. This may not work for everyone but i believe it will work for most of the persons

plumed_scripts