unanswered lipids

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12 years 8 months ago #760 by c.poojari
lipids was created by c.poojari
Dear Marrink,

I have downloaded the latest version of lipid itp files. Also contacted Cesar Lopez for Phosphatidylinositol lipids.

I want to setup a mixed bilayer simulation with 1500 lipids (3 different lipids, cholesterol and sphingolpids). Based on area per lipid, for 1500 lipids i got box dimensions of 32.5 X 32.5 X 8 nm. As i was going through one of your papers on "Simulation of Domain Formation in DLPCu2212DSPC Mixed Bilayers" you had used 2048 lipids with box dimension of 22 X 23 X 8 nm.

Please can I know how do i calculate proper box dimension for lipids ???

While generating desired number of lipids starting from a single lipid as mentioned in the tutorial, should i have same box size for all the lipids, cholesterol and sphingolipids as i want to cat them later so that i have one large box containing all the lipids and then do minimization.

or is there any other way where i can add all the different number of lipids and simulate them for self assembly.


Kind Regards,
chetan.

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