ADicksonLab / CSNAnalysis
Tools for creating, analyzing and visualizing Conformation Space Networks
☆16Updated 2 years ago
Related projects: ⓘ
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆33Updated 2 years ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆39Updated 2 years ago
- pKa estimates for proteins using an ensemble approach☆25Updated last month
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆23Updated 4 years ago
- In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes☆31Updated 3 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆39Updated 2 years ago
- Solvation Structure and Thermodynamic Mapping☆38Updated 5 months ago
- Lee-Ping's general purpose script for running OpenMM molecular dynamics simulations☆24Updated 4 months ago
- Analysis of non-covalent interactions in MD trajectories☆51Updated last year
- ☆41Updated 2 years ago
- Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.☆14Updated 6 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆51Updated 7 months ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆36Updated 5 months ago
- ☆14Updated 2 years ago
- Tutorials and additional documentation for the WESTPA suite☆13Updated last month
- Modeling molecular ensembles with scalable data structures and parallel computing☆33Updated last week
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated 11 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆22Updated 11 months ago
- Calculation of water/solvent partition coefficients with Gromacs.☆25Updated 7 months ago
- Ensembler is a python package that provides fast and easy access to 1D and 2D model system simulations. It can be used for method develop…☆49Updated 4 months ago
- ☆15Updated 7 years ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆26Updated 4 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated 10 months ago
- A tool for setting up free energy simulations.☆34Updated last year
- Physical validation of molecular simulations☆55Updated 2 months ago
- Fast PBC wrapping and unwrapping for VMD☆23Updated 6 months ago
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆19Updated 4 years ago
- RESP with inter- and intra-molecular constraints in Psi4.☆28Updated last year
- ☆19Updated this week
- ☆11Updated 3 months ago