invemichele / masterclass-22-03Links
Repository of the data for PLUMED Masterclass 22.3
☆13Updated 10 months ago
Alternatives and similar repositories for masterclass-22-03
Users that are interested in masterclass-22-03 are comparing it to the libraries listed below
Sorting:
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆45Updated 4 years ago
- Temperature generator for Replica Exchange MD simulations☆28Updated 2 years ago
- A python implementation of the string method with swarms of trajectories using GROMACS☆18Updated 2 years ago
- Supporting material for the paper "Data driven collective variables for enhanced sampling"☆18Updated 11 months ago
- Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package f…☆15Updated 7 months ago
- Automatic Mutual Information Noise Omission☆15Updated 7 months ago
- Graph-Based Force Fields Model to parameterize Force Fields by Graph Attention Networks☆9Updated last year
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆16Updated last year
- ☆9Updated 5 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆34Updated last year
- Automated calculation of cavity in molecular cages☆20Updated 2 months ago
- ☆22Updated last week
- Bayesian Multistate Bennett Acceptance Ratio Method☆13Updated 3 weeks ago
- Different run and analysis scripts as described in the research guides.☆13Updated 2 years ago
- Rethinking Metadynamics: From Bias Potentials to Probability Distributions☆11Updated last year
- ☆12Updated 4 months ago
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆15Updated 3 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆21Updated 10 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
- Density based object completion over PBC.☆30Updated 5 months ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆34Updated last week
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆68Updated last year
- Enhanced sampling methods for molecular dynamics simulations☆36Updated 2 years ago
- scripts for analyzing molecular dynamics trajectories using VMD☆38Updated 10 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- ☆41Updated 3 months ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Groma…☆33Updated 6 years ago
- NAMD-xtb-QMMM-interface☆11Updated 4 years ago
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆35Updated 3 years ago