Analyzing how lipids sort in tubules according to their intrinsic curvature
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Updated
Jul 23, 2024 - Python
Analyzing how lipids sort in tubules according to their intrinsic curvature
Kernel Density Estimation of radial, bond, angle, torsion angle, and improper angle distribution functions of an atomic or coarse-grained molecular system.
Code for analysing coarse grain interaction in Protein-SSDna complexes.
MD simulation models for PS-b-Q2VP
Deductive Multiscale Simulator
Includes C++ code to run Markovian Langevin equations in units compatible with the dcTMD correction scripts available at www.moldyn.uni-freiburg.de/software/software.html. In addition, a jupyter notebook can be found which estimates the error of rates at 300 K from T-boosting calculations.
A general cross-platform text-based molecule builder for ESPResSo similar to moltemplate
Repository of tutorials on Coarse-Grained Molecular Dynamics (CG-MD) using the Martini 3 force field, designed for running on Google Colab
Thesis repository on neural ordinary differential equations used for coarse-graining molecular dynamics
LAMMPS tutorials and exercises.
Use Case for the OpenModel project
Predictive collective variable discovery with deep Bayesian models for atomistic systems.
Tutorial to build a membrane with INSANE.
A mesh free molecular dynamics (MD) simulation for a fluid in an isothermal container
A library for the Analysis of Molecular Dynamics Simulations of Self Assembling Peptides. Started during an internship at CNTE, Niguarda Hospital, Milan
Microstate Sparse Reconstruction (MSR): a backmapping method that recovers all-atom structures from reduced/coarse-grained variables
Coarse-grained molecular dynamics simulation with the Single-Interaction-Site RNA model
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
NGAC
SIRAH Force Field
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