metadynamics
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CREST - A program for the automated exploration of low-energy molecular chemical space.
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Feb 14, 2025 - Fortran
Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
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Feb 11, 2021 - Shell
Using supervised machine learning to build collective variables for accelerated sampling
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Jun 26, 2018 - Jupyter Notebook
Sparse Gaussian Process Potentials
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Mar 6, 2025 - Python
Unified Free Energy Dynamics (UFED) simulations with OpenMM
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Mar 9, 2024 - Python
Cryptic pocket prediction using AlphaFold 2
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Nov 27, 2022 - Jupyter Notebook
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
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Sep 26, 2024 - Jupyter Notebook
Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package for R.
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Oct 30, 2024 - Python
Useful Collective Variables for OpenMM
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May 9, 2024 - Python
A Python package for enhancing VASP AIMD simulations and analysis
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Mar 7, 2025 - Python
Fast estimation of ion-pairing for screening electrolytes
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Aug 23, 2022 - Shell
Plumology - Tools to analyse biased molecular dynamics simulations
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Mar 16, 2018 - Python
This GitHub repo has folders required for setting up the Molecular Dynamics simulations, Metadynamics simulations, and a description of the post-processing codes that were used in the Patil et. al. PNAS 2021
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Mar 5, 2024 - Jupyter Notebook
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.
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Feb 15, 2021 - Jupyter Notebook
Simple tools for obtaining time from biased molecular dynamics simulations
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Aug 1, 2024 - Python
C++ implementation of metadynamics simulation on a potential energy surface
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Jan 13, 2019 - C++
A package to help automate molecular dynamics calculations
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Aug 15, 2018 - Python
Binary classifier as CV in enhanced sampling
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Apr 22, 2023 - Jupyter Notebook
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