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rshirshi 

How to coarse grained cholesterol?

Dear all,
        I want to run Coarse grained simulation about the lipid-polymer complex. However, I don't know clearly about how to build the coarse grained model using "Build mesostructure" and "mesomolecule". After setting the Bead type, how to build the coarse grained model ofor chloresterol? Could anyone give me some help?The pdb file of cholesterol is in attachment.

The next picture is a reference model
Coarse grained model for cholesterol
and this coarse grained model is form the following paper:
A coarse-grained molecular dynamics investigation of the phasebehavior of DPPC/cholesterol mixtures.Chemistry and Physics of Lipids, 2015,185: 88-98.
Best Answer chosen by rshi
reinierreinier
Hi rshi,

Have a look at the Visualizer tutorials
•             Building mesoscale molecules
•             Coarse graining atoms to beads
One uses the Build Mesomolecule tool, the other the Coarse Grain tool . You can use either method.

In [1] we used a 4-bead representation of cholesterol, for use in DPD.

Good luck,
Reinier

[1] Reinier L.C. Akkermans and James T. Wescott, Multiscale Modeling of Human Skin, Current Nanoscience 7, 7360742 (2011).
 

All Answers

reinierreinier
Hi rshi,

Have a look at the Visualizer tutorials
•             Building mesoscale molecules
•             Coarse graining atoms to beads
One uses the Build Mesomolecule tool, the other the Coarse Grain tool . You can use either method.

In [1] we used a 4-bead representation of cholesterol, for use in DPD.

Good luck,
Reinier

[1] Reinier L.C. Akkermans and James T. Wescott, Multiscale Modeling of Human Skin, Current Nanoscience 7, 7360742 (2011).
 
This was selected as the best answer
rshirshi
Hi, Reinier.
Thanks for your help. I can build the CG model for cholesterol.