These are codes of toy physics models that contain building blocks for understanding the concept behind EVCCPMC
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Updated
May 3, 2023 - Jupyter Notebook
These are codes of toy physics models that contain building blocks for understanding the concept behind EVCCPMC
Wrapper for LAMMPS simulation data into DLPack data structures
Input files for self-rbfe
Platform-agnostic OpenMM Forces
A one stop destination of open source tools in Computer Aided Drug Design (CADD)
Code and example notebook demostrating usage of Tangent Space Least Adaptive Clustering algorithm for molecular dynamics simulations with known collective variables
WESTPA modified scripts with NAMD
Data-driven discovery of linear molecular probes with optimal selective affinity for PFAS in water
Deep learning for collective variables.
Variationally enhanced sampling for single-particle langevin dynamics with neural network bias potentials and path collective variables. Based on OpenMM + PyTorch.
A python package for simulating sampling behaviors of enhanced sampling simulations
C++ implementation of metadynamics simulation on a potential energy surface
Wrapper for HOOMD-blue simulation data into DLPack data structures
Additional plumed plugins
Plugin for OpenMM providing simulation data wrappers as DLPack data structures
Development version of PLUMED 2 which includes the VES code for performing variationally enhanced sampling simulations
Extended Phase-Space Simulations with OpenMM
Simple tools for obtaining time from biased molecular dynamics simulations
Prediction of magnesium binding sites in RNA molecules using GCMC/MD (Updated version: https://github.com/mackerell-lab/GCMC_PME)
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