marrink-lab / vermouth-martinizeLinks
Describe and apply transformation on molecular structures and topologies
☆135Updated 2 weeks ago
Alternatives and similar repositories for vermouth-martinize
Users that are interested in vermouth-martinize are comparing it to the libraries listed below
Sorting:
- INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems☆75Updated last year
- ☆62Updated last month
- Martini 3 small molecule database☆69Updated 4 months ago
- OpenMM plugin to interface with PLUMED☆74Updated 3 weeks ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆167Updated last week
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆151Updated 2 weeks ago
- Force fields produced by the Open Force Field Initiative☆175Updated 3 weeks ago
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆135Updated last year
- clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)☆126Updated last year
- the simple alchemistry library☆232Updated last week
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆74Updated 2 years ago
- A repository containing the build steps for the ccpbiosim workshop on QM/MM☆68Updated last week
- Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates☆182Updated last month
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆91Updated 6 months ago
- Benchmark set for relative free energy calculations.☆118Updated last year
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆137Updated 2 months ago
- LiveCoMS GROMACS Tutorials Paper☆136Updated 6 years ago
- binding free energy estimator 2☆137Updated 2 weeks ago
- A python toolkit for analysing membrane protein-lipid interactions.☆69Updated 3 months ago
- OFFICIAL: AnteChamber PYthon Parser interfacE☆245Updated 3 weeks ago
- GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).☆185Updated 5 months ago
- MDANCE: O(N) clustering for molecular dynamics. Process 1.5M frames in 40min. 8 specialized algorithms.☆98Updated last week
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆166Updated last month
- ☆65Updated 6 months ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆46Updated 4 years ago
- 📐 Symmetry-corrected RMSD in Python☆110Updated last month
- Automatic MARTINI parametrization of small organic molecules☆72Updated 8 months ago
- OpenMM tutorial for the MSBS course☆183Updated last week
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆82Updated 2 years ago
- Density based object completion over PBC.☆30Updated last year