markovmodel / pyemma-workshop
☆26Updated 2 years ago
Related projects ⓘ
Alternatives and complementary repositories for pyemma-workshop
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆14Updated last year
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆19Updated 5 years ago
- ☆32Updated 2 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…☆51Updated 6 months ago
- Examples of applications of pymbar to various problems in simulation and experiment☆18Updated 9 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
- 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 4 months ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆27Updated 9 months ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆36Updated 7 months ago
- Python Tools for NAMD☆19Updated last year
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆27Updated 4 years ago
- Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium☆31Updated this week
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆55Updated 9 months ago
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆38Updated this week
- Calculation of water/solvent partition coefficients with Gromacs.☆25Updated last month
- Package for consistent reporting of relative free energy results☆37Updated 5 months ago
- Entropy from PDB conformational ensembles☆7Updated 7 months ago
- Standalone charge assignment from Espaloma framework.☆38Updated 4 months ago
- Compare optimized geometries and energies from various force fields with respect to a QM reference.☆13Updated 3 years ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆23Updated 4 years ago
- Repository for MD methods and analysis from submitted or published work☆17Updated last year
- A command line application to launch molecular dynamics simulations with OpenMM☆39Updated 2 years ago
- Python code for generating Boresch restraints from MD simulations☆18Updated 2 years ago
- Set up relative free energy calculations using a common scaffold☆22Updated 2 months ago
- ☆64Updated 10 months ago
- ☆10Updated 5 months ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆27Updated 3 weeks ago
- Enhanced sampling methods for molecular dynamics simulations☆36Updated last year
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆60Updated last year
- ☆29Updated last year