Standard molecular dynamics and metadynamics simulations of the Recoverin protein.
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Updated
May 24, 2024 - Jupyter Notebook
Standard molecular dynamics and metadynamics simulations of the Recoverin protein.
A repository for the test systems for the development of alchemical metadynamics
Deep learning for collective variables.
Auxiliary tools and scripts initially made for my PhD projects.
symbolic collective variable definitions and automation of metadynamics
A package that allows you to read COLVAR output from Plumed and access data
New implementation of TS-PPTIS working with Gromacs 5.X and Plumed 2.X
A python package for simulating sampling behaviors of enhanced sampling simulations
C++ implementation of metadynamics simulation on a potential energy surface
A package to help automate molecular dynamics calculations
Binary classifier as CV in enhanced sampling
Run metadynamics simulations and analyse free energy surfaces
Molecular Dynamics - Simulation Analysis and Preparation Suite
tICA to capture local loop motion. Describes how to analyse loop movement using TICA and how to run PT-Metad using TIC vectors
A Python package enhancing VASP AIMD simulation
How one can use binary classifiers, variational auto-encoder, TICA, PCA, distance and dihedral order parameters as CVs in context of pepsin-like aspartic proteases e.g. BACE1 and plasmepsin-II.
Files for PLUMED Masterclass-22-11
Simple tools for obtaining time from biased molecular dynamics simulations
Plumology - Tools to analyse biased molecular dynamics simulations
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