delemottelab / string-method-swarms-trajectories
A python implementation of the string method with swarms of trajectories using GROMACS
☆17Updated 2 years ago
Related projects ⓘ
Alternatives and complementary repositories for string-method-swarms-trajectories
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆41Updated 3 years ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆60Updated last year
- 📐 Symmetry-corrected RMSD in Python☆85Updated this week
- Martini 3 small-molecule database☆54Updated 3 months ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆70Updated 5 months ago
- Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)☆42Updated 4 years ago
- Supporting material for the paper "Data driven collective variables for enhanced sampling"☆15Updated 5 months ago
- Enhanced sampling methods for molecular dynamics simulations☆36Updated last year
- Temperature generator for Replica Exchange MD simulations☆25Updated last year
- Repository for the 2024 OpenFE industry benchmark efforts☆12Updated this week
- RESP with inter- and intra-molecular constraints in Psi4.☆29Updated last year
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆61Updated this week
- Set up relative free energy calculations using a common scaffold☆22Updated 2 months ago
- ☆64Updated 10 months ago
- Automatic Mutual Information Noise Omission☆14Updated last month
- ☆59Updated this week
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated last year
- Automatic MARTINI parametrization of small organic molecules☆61Updated 2 weeks ago
- Advanced toolkit for binding free energy calculations☆31Updated last month
- Machine Learning model for molecular micro-pKa prediction☆32Updated last month
- ☆49Updated last year
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆31Updated 3 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆14Updated last year
- ☆26Updated last month
- A fast solver for large scale MBAR/UWHAM equations☆37Updated 2 months ago
- A python class for building a ZMatrix from a RDKit molecule. We can also do coordinate transformations between ZMatrix and Cartesian spac…☆13Updated last year
- Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-…☆43Updated 3 months ago
- ☆93Updated 2 months ago