C++ implementation of metadynamics simulation on a potential energy surface
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Updated
Jan 13, 2019 - C++
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
Fast estimation of ion-pairing for screening electrolytes
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.
Molecular Dynamics - Simulation Analysis and Preparation Suite
Standard molecular dynamics and metadynamics simulations of the Recoverin protein.
tICA to capture local loop motion. Describes how to analyse loop movement using TICA and how to run PT-Metad using TIC vectors
A package that allows you to read COLVAR output from Plumed and access data
symbolic collective variable definitions and automation of metadynamics
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
Run metadynamics simulations and analyse free energy surfaces
Files for PLUMED Masterclass-22-11
Useful Collective Variables for OpenMM
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
Cryptic pocket prediction using AlphaFold 2
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