SIRAH Force Field
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Updated
Sep 30, 2024
SIRAH Force Field
The source of the votca-csg and xtp packages
Repository of tutorials on Coarse-Grained Molecular Dynamics (CG-MD) using the Martini 3 force field, designed for running on Google Colab
C++ package that provides tools for correcting structural predictions of proteins (eg. from X-Ray Crystallography or AlphaFold) using X-ray small-angle scattering (SAXS) in solution
Coarse-grained molecular dynamics simulation with the Single-Interaction-Site RNA model
Kernel Density Estimation of radial, bond, angle, torsion angle, and improper angle distribution functions of an atomic or coarse-grained molecular system.
COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies
Analyzing how lipids sort in tubules according to their intrinsic curvature
End-To-End Molecular Dynamics (MD) Engine using PyTorch
LAMMPS tutorials and exercises.
COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM
[TMLR 2023] Simulate time-integrated coarse-grained MD with multi-scale graph neural networks
A library for the Analysis of Molecular Dynamics Simulations of Self Assembling Peptides. Started during an internship at CNTE, Niguarda Hospital, Milan
Code for analysing coarse grain interaction in Protein-SSDna complexes.
Use Case for the OpenModel project
Thesis repository on neural ordinary differential equations used for coarse-graining molecular dynamics
Tools to build coarse grained models and perform simulations with OpenMM
Generate coarse-grained molecular dynamics models from atomistic trajectories.
Deductive Multiscale Simulator
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