I want to simulate a niosome bilayer with schrodinger software (molecular dynamics), but first I have to design the proper bilayer. Does anyone know a software or simulator to design a bilayer with a certain composition?
There is a VMD (visual molecular dynamics, https://www.ks.uiuc.edu/Research/vmd/) Plug-in to help set up membranes for the MD simulation of membrane proteins
https://www.ks.uiuc.edu/Research/vmd/plugins/membrane/
Tutorial:
http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/mem-tutorial.pdf
There is a VMD (visual molecular dynamics, https://www.ks.uiuc.edu/Research/vmd/) Plug-in to help set up membranes for the MD simulation of membrane proteins
https://www.ks.uiuc.edu/Research/vmd/plugins/membrane/
Tutorial:
http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/mem-tutorial.pdf
Thank you so much dear @Annemarie Honegger. Could it be read by schrodinger?
It will produce pdb (coordinates) and psf (topology/parameter) files https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node23.html
dear Dr Annemarie Honegger and dear Anas Alobaidi I want to build a membrane consisted of Span60 and Tween60 and even more surfactants. what should I write instead of the lipid-name in the command?
The library of pre-defined lipids for the VMD membrane plug-in seems somewhat limited, you will have to check the documentation to find out what is available. If you cannot find the answer to your question in the program documentation and tutorials, the best place to ask is in the VMD mailing list : https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/
That is the best place to reach the experts.
You might also have look at this:
http://www.charmm-gui.org/?doc=input/membrane.bilayer , they seem to have determined parameters for a far larger variety of lipids.
This seems to be a fairly decent overview over tools for membrane simulation:
Article Efficient preparation and analysis of Membrane And Membrane ...
For more information, Google: https://www.google.com/search?client=safari&rls=en&q=membrane+simulation+tool&ie=UTF-8&oe=UTF-8
You may also want to explore this site (Membrane Protein Structural Dynamics Gateway: http://memprotein.org)
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