sosnicklab / upside2-mdLinks
☆24Updated this week
Alternatives and similar repositories for upside2-md
Users that are interested in upside2-md are comparing it to the libraries listed below
Sorting:
- Coarse-grained molecular dynamics for protein physics. NOTE: this has been superseded by Upside 2: https://github.com/sosnicklab/upside2-…☆23Updated 3 years ago
- ☆54Updated 2 years ago
- ☆64Updated this week
- Convert coarse-grained protein structure to all-atom model☆38Updated 11 months ago
- Force fields in various formats☆26Updated last year
- Python implementation of Dynamical Network Analysis☆13Updated 2 months ago
- Trusted force field files for gromacs☆50Updated 7 months ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆73Updated this week
- ☆68Updated 11 months ago
- EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling☆25Updated last week
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆81Updated last month
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- Modeling with limited data☆57Updated 6 months ago
- Random Acceleration Molecular Dynamics in GROMACS☆37Updated 10 months ago
- A fast solver for large scale MBAR/UWHAM equations☆39Updated 9 months ago
- Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching☆7Updated 2 weeks ago
- ☆31Updated 7 months ago
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆35Updated 3 years ago
- Temperature generator for Replica Exchange MD simulations☆28Updated 2 years ago
- ☆22Updated 2 weeks ago
- Simple protein-ligand complex simulation with OpenMM☆85Updated last year
- ☆65Updated last year
- Force Fields☆62Updated 4 months ago
- Analysis of non-covalent interactions in MD trajectories☆57Updated 5 months ago
- some scripts for analysis of MD and CADD. And some tutorials.☆54Updated 9 months ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆16Updated 2 years ago
- Interactive molecular dynamics based model building into low-resolution crystallographic and cryo-EM maps☆38Updated 3 weeks ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆69Updated 4 months ago
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2