Density based object completion over PBC.
☆31Apr 23, 2026Updated last month
Alternatives and similar repositories for mdvwhole
Users that are interested in mdvwhole are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆28Jan 20, 2022Updated 4 years ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆49May 22, 2026Updated last week
- The OpenMM Cookbook and Tutorials☆57Apr 28, 2026Updated last month
- MDAnalysis tool to calculate membrane curvature.☆35Updated this week
- Software for automated processing of alchemical free energy calculations☆12Nov 7, 2022Updated 3 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- C++ toolkit for use in reading in and analyzing Gromacs files☆13Oct 3, 2020Updated 5 years ago
- Data and script of Umbrella Sampling for molecular transmembrane☆14Jun 21, 2024Updated last year
- Generates Martini models for open carbon nanotubes to use with Gromacs.☆15Nov 24, 2021Updated 4 years ago
- This is a short tutorial showing how to use both VMD and MDAnalysis to analyse a molecular dynamics simulation of a membrane protein.☆28Oct 1, 2020Updated 5 years ago
- A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling metho…☆24Sep 26, 2024Updated last year
- A voxel based approach for dynamic cluster analysis of molecular dynamics trajectories.☆32Nov 5, 2025Updated 6 months ago
- Martini 3 Building Blocks for Lipid Nanoparticle Design☆26Mar 18, 2026Updated 2 months ago
- Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters.☆16Dec 20, 2022Updated 3 years ago
- Wrapper script for preparing explicitly solvated systems for molecular dynamics simulations with Amber.☆17Feb 6, 2026Updated 3 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- the simple alchemistry test set☆10Nov 20, 2025Updated 6 months ago
- TS2CG version 2☆27Apr 18, 2026Updated last month
- VMD Plugin and associated scripts to build lignin structures from topological specifications☆17Jul 17, 2025Updated 10 months ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆16Mar 17, 2026Updated 2 months ago
- Some of useful tcl scripts to analyse data from VMD☆15Aug 2, 2022Updated 3 years ago
- Temperature generator for Replica Exchange MD simulations☆30Dec 14, 2022Updated 3 years ago
- Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations☆20Feb 25, 2026Updated 3 months ago
- A ready-to-use energy diagram drawing program☆13Nov 23, 2023Updated 2 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆29Dec 4, 2024Updated last year
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Multiscale Simulation Tool for Backmapping☆22Mar 13, 2026Updated 2 months ago
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆25Jun 8, 2024Updated last year
- Scripts for PCA and related analyses of lipid motions☆10Jun 21, 2022Updated 3 years ago
- ☆65Dec 10, 2025Updated 5 months ago
- GROM is a GROMACS(mdp,itp,top) files with Syntax Highlighting and PDB Editor with visual cues in one package based on Qt5,PyQt5 and Pyth…☆11Nov 14, 2016Updated 9 years ago
- Analysis of non-covalent interactions in MD trajectories☆69Jan 3, 2025Updated last year
- Example files for Colvars module: https://github.com/Colvars/colvars☆14Dec 7, 2021Updated 4 years ago
- ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI☆22Jul 28, 2025Updated 10 months ago
- GridMAT-MD membrane analysis program☆26Sep 15, 2018Updated 7 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆11Oct 18, 2019Updated 6 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Jan 16, 2015Updated 11 years ago
- Convenience functions for VMD-TCL scripting☆14Apr 3, 2026Updated last month
- Input files for GROMACS tutorials written for the Journal of Physical Chemistry B☆25Jul 21, 2024Updated last year
- Notebooks for NYU Statistical Mechanics☆20Jul 6, 2023Updated 2 years ago
- easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems an…☆40May 21, 2026Updated last week
- Thermodynamically Explainable Representations of AI and other black-box Paradigms☆35Nov 3, 2024Updated last year