I saw that in Packmol I can create initial configuration for bilayers and spherical structures, but is it possible to create cylinder structures? I want to create reversed hexagonal phase (HII in attachment indeks.jpeg). Is it possible to do this in packmol or maybe you know any other programs, which could help me?
If I will not find, I will probably use pymol script to build that.
Jakub Hryc My former lab partner, Kevin Boyd PhD, created a tool in python called BUMPy (Building Unique Membranes in Python) to create membranes of all kinds of shapes. Inverted cylinders should be feasible.
Here's the original article if your interested: Article BUMPy: A Model-Independent Tool for Constructing Lipid Bilay...
And the github repository: https://github.com/MayLab-UConn/BUMPy
And some examples of the shapes he made using the tool:
VMD program can be employed to that:
https://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node169.html
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