Tutorial to build a membrane with INSANE.
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Updated
Jan 31, 2018 - Makefile
Tutorial to build a membrane with INSANE.
NGAC
A general cross-platform text-based molecule builder for ESPResSo similar to moltemplate
A mesh free molecular dynamics (MD) simulation for a fluid in an isothermal container
Predictive collective variable discovery with deep Bayesian models for atomistic systems.
Microstate Sparse Reconstruction (MSR): a backmapping method that recovers all-atom structures from reduced/coarse-grained variables
MD simulation models for PS-b-Q2VP
Example to fit parameters and run CG simulations using TorchMD and Schnet
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.
Deductive Multiscale Simulator
Generate coarse-grained molecular dynamics models from atomistic trajectories.
Tools to build coarse grained models and perform simulations with OpenMM
Thesis repository on neural ordinary differential equations used for coarse-graining molecular dynamics
Use Case for the OpenModel project
Code for analysing coarse grain interaction in Protein-SSDna complexes.
A library for the Analysis of Molecular Dynamics Simulations of Self Assembling Peptides. Started during an internship at CNTE, Niguarda Hospital, Milan
[TMLR 2023] Simulate time-integrated coarse-grained MD with multi-scale graph neural networks
COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM
LAMMPS tutorials and exercises.
End-To-End Molecular Dynamics (MD) Engine using PyTorch
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