Topic: "metadynamics"
crest-lab/crest
CREST - A program for the automated exploration of low-energy molecular chemical space.
Language: Fortran - Size: 2.04 MB - Last synced at: 3 days ago - Pushed at: about 1 month ago - Stars: 269 - Forks: 50
NNairIITK/Enhanced_Sampling_Methods_Tutorials
Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
Language: Shell - Size: 3.78 MB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 44 - Forks: 17
svats73/mdml
mdml: Deep Learning for Molecular Simulations
Language: Python - Size: 5.92 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 34 - Forks: 7
amirhajibabaei/AutoForce
Sparse Gaussian Process Potentials
Language: Python - Size: 1.68 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 27 - Forks: 13
msultan/SML_CV
Using supervised machine learning to build collective variables for accelerated sampling
Language: Jupyter Notebook - Size: 140 MB - Last synced at: over 2 years ago - Pushed at: about 7 years ago - Stars: 22 - Forks: 4
craabreu/ufedmm
Unified Free Energy Dynamics (UFED) simulations with OpenMM
Language: Python - Size: 2.08 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 21 - Forks: 9
weitse-hsu/enhanced_sampling_tutorials
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
Language: Jupyter Notebook - Size: 4.93 MB - Last synced at: 24 days ago - Pushed at: 12 months ago - Stars: 20 - Forks: 2
Jan8be/metadynminer.py
Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package for R.
Language: Python - Size: 45 MB - Last synced at: 8 days ago - Pushed at: 10 months ago - Stars: 18 - Forks: 6
RedesignScience/cvpack
Useful Collective Variables for OpenMM
Language: Python - Size: 6.68 MB - Last synced at: 18 days ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 2
jcwang587/xdatbus 📦
Python package for enhancing VASP AIMD simulations and analysis
Language: Python - Size: 42 MB - Last synced at: about 17 hours ago - Pushed at: 2 months ago - Stars: 13 - Forks: 2
sbhakat/AF-cryptic-pocket
Cryptic pocket prediction using AlphaFold 2
Language: Jupyter Notebook - Size: 72.9 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 11 - Forks: 2
ajaymur91/CLIPS
Fast estimation of ion-pairing for screening electrolytes
Language: Shell - Size: 17.8 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 9 - Forks: 0
KesPatil/ALK_files_2021_PNAS
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
Language: Jupyter Notebook - Size: 7.84 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 3
tlhr/plumology
Plumology - Tools to analyse biased molecular dynamics simulations
Language: Python - Size: 124 KB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 6 - Forks: 2
valsson-group/time-from-biased-simulations-tools
Simple tools for obtaining time from biased molecular dynamics simulations
Language: Python - Size: 10.6 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 5 - Forks: 4
sbhakat/PAP-review-inputs
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.
Language: Jupyter Notebook - Size: 12 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 3
NNairIITK/Vreco_CPMD
CPMD Free Energy Surface Reconstruction
Language: Roff - Size: 8.32 MB - Last synced at: 5 days ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 1
rangsimanketkaew/deepcv
Mirror repository of "Deep learning for collective variables" https://gitlab.uzh.ch/lubergroup/deepcv
Language: Python - Size: 2.67 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 2 - Forks: 0
ravenswing/phd_tools
Auxiliary tools and scripts initially made for my PhD projects.
Language: Jupyter Notebook - Size: 167 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 0
ravenswing/mdsaps
Molecular Dynamics - Simulation Analysis and Preparation Suite
Language: Python - Size: 1020 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 2 - Forks: 0
sbhakat/Classifier-CV-sampling
Binary classifier as CV in enhanced sampling
Language: Jupyter Notebook - Size: 7.49 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0
sbhakat/BPTI-TICA-waterdynamics
tICA to capture local loop motion. Describes how to analyse loop movement using TICA and how to run PT-Metad using TIC vectors
Language: Jupyter Notebook - Size: 21.3 MB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 0
theavey/AutoMet
A package to help automate molecular dynamics calculations
Language: Python - Size: 302 KB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 0
weitse-hsu/sampling_simulator
A python package for simulating sampling behaviors of enhanced sampling simulations
Language: Python - Size: 1.26 MB - Last synced at: 24 days ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
weitse-hsu/MetaD_EXE_TestSys
A repository for the test systems for the development of alchemical metadynamics
Language: Python - Size: 24.2 GB - Last synced at: 24 days ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
sbhakat/colvar
A package that allows you to read COLVAR output from Plumed and access data
Language: Python - Size: 6.84 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0
hejops/metadynamics
Run metadynamics simulations and analyse free energy surfaces
Language: Python - Size: 85 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0
danieljsharpe/metadynamics
C++ implementation of metadynamics simulation on a potential energy surface
Language: C++ - Size: 69.3 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0
ucl-tspptis/TS-PPTIS
New implementation of TS-PPTIS working with Gromacs 5.X and Plumed 2.X
Language: Python - Size: 74.4 MB - Last synced at: almost 2 years ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 0
Komputerowe-Projektowanie-Lekow/pmarlo
https://pypi.org/project/pmarlo/
Language: Python - Size: 26.7 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0
salvatoredimarco/rna-membrane
Additional data for the manuscript "All-atom simulations elucidate the molecular mechanism underlying RNA-membrane interactions"
Language: Jupyter Notebook - Size: 418 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
alicejpettitt/thesis_2024
Scripts from my PhD for a thesis published by University College London
Language: Jupyter Notebook - Size: 117 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
ianrgraham/hoomd-mimse
GPU-accelerated metadynamics code for obtaining low energy states
Language: Python - Size: 189 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
Peppone98/Simulations_Recoverin
Standard molecular dynamics and metadynamics simulations of the Recoverin protein. Master's degree thesis @ Unitn
Language: Jupyter Notebook - Size: 1.2 GB - Last synced at: 4 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
valsson-group/masterclass-22-11
Files for PLUMED Masterclass-22-11
Language: Jupyter Notebook - Size: 287 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
amirhajibabaei/easy-meta-md
symbolic collective variable definitions and automation of metadynamics
Language: Python - Size: 66.4 KB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0