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abacus-develop

An electronic structure package based on either plane wave basis or numerical atomic orbitals.

alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations

alchemlyb

the simple alchemistry library

angus

benchmarksets

Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards

community

DeepModeling community content

deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

dflow

dflow-phonon

dflow_phonon

Phonon computing workflow based on dflow

dmff

DMFF (Differentiable Molecular Force Field) is a Jax-based python package that provides a full differentiable implementation of molecular force field models.

docs

dp-gen-tutorial

This is an easy tutorial of DP-GEN

dp_software

easy test for softwares relevant to deepmd

dpdata

Manipulating DeePMD-kit, VASP, LAMMPS data formats.

dpdispatcher

dpgen

The deep potential generator

dpgen2

fep-benchmark

Benchmark set for relative free energy calculations.

fpop

gromacswrapper

GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools (v4.6.x, v5.x, 2016.x, 2018.x, 2019.x, all with the same Python code) into python scripts.

input_ti

ising-gpu

GPU Accelerated Monte Carlo Simulations of the 2D Ising Model

lammps-dp-feedstock

A conda-smithy repository for lammps-dp.

lysozyme_binding

Aggregator of binding data of small molecules to model binding sites in T4 lysozyme mutants, as popularized by Matthews, Shoichet and others.

metadmodel

Package for simulating simple models of metadynamics and replica exchange simulations.

nglview

Jupyter widget to interactively view molecular structures and trajectories

parmed

Parameter/topology editor and molecular simulator

parrallel_computation

pmx

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling