delemottelab / string-method-swarms-trajectoriesLinks
A python implementation of the string method with swarms of trajectories using GROMACS
☆18Updated 3 years ago
Alternatives and similar repositories for string-method-swarms-trajectories
Users that are interested in string-method-swarms-trajectories are comparing it to the libraries listed below
Sorting:
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆75Updated 2 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Updated 5 years ago
- Martini 3 small molecule database☆70Updated 4 months ago
- Repository of the data for PLUMED Masterclass 22.3☆14Updated last year
- OpenMM plugin to interface with PLUMED☆74Updated 3 weeks ago
- Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)☆45Updated 5 years ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 3 years ago
- Automatic MARTINI parametrization of small organic molecules☆72Updated 8 months ago
- Automatic Mutual Information Noise Omission☆15Updated last year
- ☆65Updated 6 months ago
- MDANCE: O(N) clustering for molecular dynamics. Process 1.5M frames in 40min. 8 specialized algorithms.☆98Updated 2 weeks ago
- Repository for the 2024 OpenFE industry benchmark efforts☆31Updated 4 months ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 4 months ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated 2 years ago
- ☆21Updated last month
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆40Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- Density based object completion over PBC.☆30Updated last year
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆72Updated 2 weeks ago
- 📐 Symmetry-corrected RMSD in Python☆110Updated last month
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆19Updated 2 years ago
- A tool for setting up free energy simulations.☆36Updated 3 years ago
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago
- ☆62Updated 2 months ago
- Machine Learning model for molecular micro-pKa prediction☆51Updated last year
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆16Updated 4 years ago
- Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-…☆46Updated last year
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆34Updated 7 months ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆16Updated 3 months ago
- ☆31Updated 2 weeks ago