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mixed bilayer
#25988 12/11/10 04:05 PM
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Dear all,

I have simulated the pure lipid bilayer of 2 systems, and I now would like to build the mixed lipid bilayer.

could anyone please suggest me

how can I replace the lipid randomely (say model A) with the lipid that I selected from the another model (say model B)?

Thank you very much.

Re: mixed bilayer
beginner #25990 12/11/10 04:44 PM
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rmv Online Content
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It depends on what is meant by "model A" and "model B", but often it's best to build new bilayer models, using the previous simulations as a source of individual lipid conformations.


Rick Venable
computational chemist

Re: mixed bilayer
rmv #25992 12/12/10 06:05 AM
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Thank you very much Rick.

My aim is to build the bilayers with different ratio of A and B.

My plan is (i)delete a certain number of lipid A and (ii) replace it with lipid B (randomely select from model B). However I have no idea how to do it with CHARMM.

As I would like to keep the conformation of lipid B, I do not think that it would be a goos idea to modify the crd/pdb file of lipid A --> B .

Any suggestions please?

Re: mixed bilayer
beginner #25993 12/12/10 06:55 PM
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rmv Online Content
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Same as before-- pack new bilayers using equilbrated conformations of individual A and B molecules. Inserting molecules into an existing bilayer is not that easy.


Rick Venable
computational chemist


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