apallath / WHAM
Python package to construct free energy profiles from biased molecular simulation data using both log-likelihood maximization and self-consistent iteration approaches.
☆16Updated 9 months ago
Alternatives and similar repositories for WHAM:
Users that are interested in WHAM are comparing it to the libraries listed below
- Repository for MD methods and analysis from submitted or published work☆17Updated last year
- ☆10Updated 5 years ago
- Enhanced sampling methods for molecular dynamics simulations☆36Updated 2 years ago
- OpenMM plugin for simulating electrochemical systems☆15Updated 6 months ago
- ☆16Updated 5 months ago
- A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling metho…☆15Updated 6 months ago
- Materials for the 2021 PRACE Workshop @ SurfSARA☆30Updated 3 years ago
- A simple implementation of replica exchange MD simulations for OpenMM.☆23Updated 3 years ago
- A Package for Parametrization of Molecular Mechanics Force Fields☆31Updated 2 years ago
- Plug-in for ChimeraX providing features for building and manipulating organic and organometallic molecules as well as displaying output f…☆26Updated 2 weeks ago
- RESP with inter- and intra-molecular constraints in Psi4.☆30Updated last year
- ☆58Updated 4 months ago
- Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-…☆45Updated 7 months ago
- MLP training for molecular systems☆46Updated last week
- Collection of interaction and molecule parameters for the Martini3 force-field☆13Updated 2 years ago
- Poltype 2: Automated Parameterization for AMOEBA☆44Updated this week
- Development of High-Throughput Polymer Network Atomistic Simulation☆19Updated 4 months ago
- scripts for analyzing molecular dynamics trajectories using VMD☆38Updated 9 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆20Updated 10 years ago
- Supporting material for the paper "Data driven collective variables for enhanced sampling"☆18Updated 9 months ago
- Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Groma…☆33Updated 6 years ago
- AutoTST: A framework to perform automated transition state theory calculations☆37Updated 7 months ago
- ☆33Updated 6 months ago
- MDAnalysis wrapper around Packmol☆30Updated last year
- Mindless molecule generator in a Python package.☆22Updated this week
- autoDIAS: a python tool for an automated Distortion/Interaction Activation Strain Analysis☆16Updated 3 years ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆31Updated 5 years ago
- Python program for modelling and simulating polymers.☆33Updated 2 weeks ago
- ☆12Updated 2 months ago
- Physical validation of molecular simulations☆56Updated 2 months ago