ChenGiuseppe / PyMM
A Python program for QM/MM Simulations based on the Perturbed Matrix Method
☆25Updated last year
Alternatives and similar repositories for PyMM:
Users that are interested in PyMM are comparing it to the libraries listed below
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆28Updated last year
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆22Updated 9 months ago
- ☆33Updated 6 months ago
- Weighted Ensemble Data Analysis and Plotting☆23Updated 6 months ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆31Updated 5 years ago
- ☆27Updated 9 months ago
- Data set of protein-ligand complexes with reliable experimental structures and affinities☆29Updated last month
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆21Updated last year
- Multiscale Simulation Tool for Backmapping☆16Updated 2 weeks ago
- A collections of scripts for working molecular dynamics simulations☆42Updated 10 months ago
- ☆18Updated 3 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 2 years ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆15Updated 8 months ago
- ☆15Updated 2 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆28Updated 2 weeks ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆36Updated 2 years ago
- The pDynamo molecular modeling and simulation program☆36Updated 3 weeks ago
- ☆21Updated 6 months ago
- Implementation of Shape and Electrostatic similarity metric in deepFMPO.☆43Updated 3 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Standalone charge assignment from Espaloma framework.☆39Updated 8 months ago
- Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.☆9Updated 8 months ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆37Updated 11 months ago
- ☆29Updated last year
- PyL3dMD: Python LAMMPS 3D Molecular Descriptors Package☆28Updated 8 months ago
- McDock: Simple Monte Carlo docking algorithm in C++☆10Updated 8 years ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆17Updated 4 years ago
- Cloud-based Drug Binding Structure Prediction☆35Updated 2 weeks ago
- ☆25Updated last year