markovmodel / graphtime
Encoding of transition probabilities with undirected graphical models
☆9Updated 6 years ago
Alternatives and similar repositories for graphtime:
Users that are interested in graphtime are comparing it to the libraries listed below
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 2 years ago
- Enhanced sampling methods for molecular dynamics simulations☆36Updated 2 years 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…☆52Updated 10 months ago
- A fast solver for large scale MBAR/UWHAM equations☆38Updated 6 months ago
- Repository for MD methods and analysis from submitted or published work☆17Updated last year
- A stripped-down set of just antechamber, sqm, and tleap.☆30Updated 3 years ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆43Updated 3 years ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆38Updated 11 months ago
- ☆15Updated 2 years ago
- ☆43Updated 3 years ago
- Get access to our MD data files.☆28Updated last year
- Experimental small molecule hydration free energy dataset☆30Updated 2 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆58Updated last year
- Fast PBC wrapping and unwrapping for VMD☆23Updated 4 months ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆31Updated 5 years ago
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆33Updated this week
- Best practice document for alchemical free energy calculations going to livecoms journal☆69Updated last month
- Automatic Mutual Information Noise Omission☆14Updated 5 months ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 4 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Modeling molecular ensembles with scalable data structures and parallel computing☆34Updated last month
- Main repository for METAGUI3☆18Updated 3 years ago
- Model Evaluation Toolkit☆26Updated 5 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆26Updated 5 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆24Updated 3 months ago
- ☆13Updated 5 years ago
- Set up relative free energy calculations using a common scaffold☆22Updated 7 months ago
- Physical validation of molecular simulations☆56Updated 2 months ago
- Copernicus☆17Updated 7 years ago
- OpenMM plugin to define forces with neural networks☆32Updated 5 years ago