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Posted By: mzzt Bilayer Center - 07/22/08 05:25 PM
Dear Charmm users,

I did a simulation of a lipid bilayer by keeping the bilayer center at 0,0,0 while system setup. But while production run, since there was no constraint on the bilayer at all, so is the center of bilayer still 0,0,0?

I wish to calculate the average distance between a methyl carbon atom of DMPC (i.e. say C13) and bilayer center. Simply evaluating the Z coordinate of C13 does not sound appropriate!! Kindly help.

Posted By: rmv Re: Bilayer Center - 07/22/08 05:38 PM
I often use the symmetry of the time series for the Z coords of the P atoms for each leaflet as a quick gauge of drift through the course of a simulation. It's a quick and easy analysis with CORREL, indicated by the commands below--

define leafa sele type P .and. prop Z .gt. 0. end
define leafb sele type P .and. prop Z .lt. 0. end
correl ...
enter lfa atom Z sele leafa end
enter lfb atom Z sele leafb end
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