jag1g13 / pycgtool
Generate coarse-grained molecular dynamics models from atomistic trajectories.
☆61Updated 2 years ago
Alternatives and similar repositories for pycgtool:
Users that are interested in pycgtool are comparing it to the libraries listed below
- Physical validation of molecular simulations☆56Updated last month
- Martini 3 small-molecule database☆56Updated 5 months ago
- scripts for analyzing molecular dynamics trajectories using VMD☆37Updated 9 years ago
- ☆61Updated last month
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆64Updated last year
- A comprehensive tool for analyzing liquid solvation structure.☆46Updated 6 months ago
- Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations☆20Updated 6 years ago
- Suite of programs to perform non-linear dimensionality reduction -- sketch-map in particular☆46Updated 4 months ago
- Automatic MARTINI parametrization of small organic molecules☆63Updated 2 months ago
- Quantum Mechanical Bespoke Force Field Derivation Toolkit☆95Updated 7 months ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆63Updated this week
- Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Groma…☆32Updated 6 years ago
- Python version of the modified Seminario method code☆16Updated 4 years ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆42Updated 3 years ago
- OpenMM plugin to interface with PLUMED☆64Updated 3 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆43Updated 4 years ago
- ASH is a Python-based computational chemistry and QM/MM environment, primarily for molecular calculations in the gas phase, explicit sol…☆66Updated this week
- Enhanced sampling methods for molecular dynamics simulations☆36Updated 2 years ago
- ☆57Updated 2 months ago
- Best Practices article intended for LiveCoMS☆38Updated 5 years ago
- Analysis of non-covalent interactions in MD trajectories☆51Updated last month
- Materials for the 2021 PRACE Workshop @ SurfSARA☆31Updated 3 years ago
- A Package for Parametrization of Molecular Mechanics Force Fields☆31Updated 2 years ago
- Pyssian is an object oriented library for parsing Gaussian logfiles and input files which aims to facilitate the everyday scripting of co…☆19Updated last week
- A python script to prepare GROMACS input files using INTERFACE forcefield☆23Updated 2 years ago
- Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-…☆44Updated 5 months ago
- Supporting material for the paper "Data driven collective variables for enhanced sampling"☆16Updated 8 months ago
- GridMAT-MD membrane analysis program