leeping / OpenMM-MDLinks
Lee-Ping's general purpose script for running OpenMM molecular dynamics simulations
☆31Updated last year
Alternatives and similar repositories for OpenMM-MD
Users that are interested in OpenMM-MD are comparing it to the libraries listed below
Sorting:
- Q6 Repository -- EVB, FEP and LIE simulator.☆35Updated 2 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆34Updated 3 months ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 3 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Updated last year
- ☆28Updated 7 months ago
- pKa estimates for proteins using an ensemble approach☆29Updated 5 months ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆30Updated last year
- Computational Chemistry Workflows☆56Updated 3 years ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆34Updated 6 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Data set of protein-ligand complexes with reliable experimental structures and affinities☆44Updated 2 months ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆32Updated 6 months ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- ☆35Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆39Updated 2 years ago
- Free Parametrization for Small Molecules☆49Updated 2 months ago
- A collections of scripts for working molecular dynamics simulations☆44Updated 4 months ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- Set up relative free energy calculations using a common scaffold☆24Updated 4 months ago
- ☆14Updated 5 months ago
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆19Updated 6 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated last year
- ☆34Updated last year
- Analysis of non-covalent interactions in MD trajectories☆66Updated 11 months ago
- A tutorials suite for BioSimSpace.☆31Updated 2 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Updated 2 years ago
- ☆25Updated last year
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆58Updated last week
- PyL3dMD: Python LAMMPS 3D Molecular Descriptors Package☆31Updated last year