plumed/plumed2

Development version of plumed 2

Language: C++ - Size: 184 MB - Last synced at: 2 days ago - Pushed at: 5 days ago - Stars: 427 - Forks: 302

Colvars/colvars

Collective variables library for molecular simulation and analysis programs

Language: C++ - Size: 42.6 MB - Last synced at: about 8 hours ago - Pushed at: about 10 hours ago - Stars: 222 - Forks: 58

molmod/psiflow

scalable molecular simulation

Language: Python - Size: 25.7 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 136 - Forks: 13

luigibonati/mlcolvar

A unified framework for machine learning collective variables for enhanced sampling simulations

Language: Python - Size: 100 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 108 - Forks: 30

SSAGESLabs/PySAGES

Python Suite for Advanced General Ensemble Simulations

Language: Python - Size: 59.4 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 82 - Forks: 27

SSAGESproject/SSAGES

Software Suite for Advanced General Ensemble Simulations

Language: C++ - Size: 67.6 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 76 - Forks: 28

ADicksonLab/wepy

Weighted Ensemble simulation framework in Python

Language: Python - Size: 49.2 MB - Last synced at: 18 days ago - Pushed at: 21 days ago - Stars: 54 - Forks: 20

msultan/vde_metadynamics

Enhanced protein mutational sampling using time-lagged variational autoencoders

Language: Python - Size: 87.2 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 26 - Forks: 6

danieljsharpe/DISCOTRESS

🦜 DISCOTRESS 🦜 is a software package to simulate and analyse the dynamics on arbitrary Markov chains

Language: C++ - Size: 4.35 MB - Last synced at: about 2 months ago - Pushed at: almost 4 years ago - Stars: 25 - Forks: 5

rinikerlab/reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.

Language: Python - Size: 77.6 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 24 - Forks: 6

msultan/SML_CV

Using supervised machine learning to build collective variables for accelerated sampling

Language: Jupyter Notebook - Size: 140 MB - Last synced at: about 2 years ago - Pushed at: almost 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: about 1 year ago - Pushed at: about 1 year ago - Stars: 21 - Forks: 9

RedesignScience/cvpack

Useful Collective Variables for OpenMM

Language: Python - Size: 6.68 MB - Last synced at: 9 days ago - Pushed at: about 1 year ago - Stars: 13 - Forks: 1

bio-phys/asyncmd

asyncmd is a library to write concurrent code for setup, run and analysis of molecular dynamics simulations using pythons async/await synthax.

Language: Python - Size: 994 KB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 11 - Forks: 4

msultan/tf_metadynamics

Using neural networks for enhanced sampling in computational biophysics

Language: Jupyter Notebook - Size: 53.2 MB - Last synced at: about 2 years ago - Pushed at: almost 8 years ago - Stars: 9 - Forks: 4

craabreu/openmm-nonbonded-slicing

An OpenMM plugin for slicing nonbonded interactions based on particle classification

Language: C++ - Size: 1.37 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 1

pedrojuanbj/MLTSA

Machine Learning Transition State Analysis (MLTSA) suite with Analytical models to create data on demand and test the approach on different types of data and ML models.

Language: Jupyter Notebook - Size: 497 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 5

ShuklaGroup/REAP-ReinforcementLearningBasedAdaptiveSampling

Language: Python - Size: 655 KB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 5 - Forks: 2

valsson-group/time-from-biased-simulations-tools

Simple tools for obtaining time from biased molecular dynamics simulations

Language: Python - Size: 10.5 MB - Last synced at: 4 months ago - Pushed at: 10 months ago - Stars: 4 - Forks: 4

aakognole/rna-mg-predictor

Prediction of magnesium binding sites in RNA molecules using GCMC/MD (Updated version: https://github.com/mackerell-lab/GCMC_PME)

Language: Shell - Size: 5.51 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 1

craabreu/openxps

Extended Phase-Space Simulations with OpenMM

Language: Python - Size: 646 KB - Last synced at: 4 days ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0

SSAGESLabs/hoomd-dlext

Wrapper for HOOMD-blue simulation data into DLPack data structures

Language: C++ - Size: 110 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 2 - Forks: 4

ves-code/plumed2-ves Fork of plumed/plumed2

Development version of PLUMED 2 which includes the VES code for performing variationally enhanced sampling simulations

Language: C++ - Size: 165 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 3

weiHelloWorld/plumed_additional

Additional plumed plugins

Language: C++ - Size: 24.4 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0

rangsimanketkaew/deepcv

Deep learning for collective variables.

Language: Python - Size: 2.21 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

wehs7661/sampling_simulator

A python package for simulating sampling behaviors of enhanced sampling simulations

Language: Python - Size: 1.26 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

buenfilstats/Molecular-Dynamics-Project

Code and example notebook demostrating usage of Tangent Space Least Adaptive Clustering algorithm for molecular dynamics simulations with known collective variables

Size: 1.93 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

Ferg-Lab/pines

Permutationally invariant networks for enhanced sampling (PINES)

Language: C++ - Size: 26.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

lexin-chen/WESTPA2.0-NAMD

WESTPA modified scripts with NAMD

Language: Shell - Size: 5.73 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

SSAGESLabs/openmm-dlext

Plugin for OpenMM providing simulation data wrappers as DLPack data structures

Language: C++ - Size: 129 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 4

delemottelab/gpcr-string-method-2019

Language: Python - Size: 31.9 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 3

danieljsharpe/metadynamics

C++ implementation of metadynamics simulation on a potential energy surface

Language: C++ - Size: 69.3 KB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

2253shubham/Gaussian_LAMMPS_ASE_for_QMMM

Gaussian + LAMMPS + ASE implementation to perform optimization, NEB and metadynamics calculations

Language: Python - Size: 105 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

pedro-tulio/pyadmd

Setup and run aMDeNM simulations with Python

Language: Python - Size: 3.7 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

pedro-tulio/amdenm

Setup, run and analyse Adaptive MDeNM simulations on CHARMM

Language: Shell - Size: 113 KB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

ladislav-hovan/comet

C++ code for optimising coefficients of individual CVs for PCV MD simulations.

Language: C++ - Size: 49.8 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

cpayal/caddtools

A one stop destination of open source tools in Computer Aided Drug Design (CADD)

Language: JavaScript - Size: 9.57 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

RedesignScience/openmm-cpp-forces

Platform-agnostic OpenMM Forces

Language: C++ - Size: 833 KB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

sheenam1509/self-rbfe

Input files for self-rbfe

Language: R - Size: 1.05 GB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

Ferg-Lab/activeLearningPFASLinear

Data-driven discovery of linear molecular probes with optimal selective affinity for PFAS in water

Language: Jupyter Notebook - Size: 35.3 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

SSAGESLabs/lammps-dlext

Wrapper for LAMMPS simulation data into DLPack data structures

Language: C++ - Size: 133 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 1

valsson-group/masterclass-22-11

Files for PLUMED Masterclass-22-11

Language: Jupyter Notebook - Size: 287 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

apallath/pyves

Variationally enhanced sampling for single-particle langevin dynamics with neural network bias potentials and path collective variables. Based on OpenMM + PyTorch.

Language: Python - Size: 101 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0