AMBER Archive (2008)

Subject: AMBER: Not integral charge increasing with number of lipids

Date: Thu Aug 07 2008 - 05:18:01 CDT

I would like to simulate a big DOPC membrane and I have built the files
dopc.prepin and dopc.frcmod using the Antechamber program.
With a small membrane, everything is OK (the total charge is zero, as it was
expected), but when the number of lipids increase (for example, with 500
lipids) the charge of the membrane becomes a not integral (for example, with
500 lipids the charge is -0.015000.
This number increases with the number of lipids, so when I have 1724 lipids is
quite high.

What could I do to correct the charge? Should I simulate the system with this
not integral charge?
Thank you very much for your help,

Best wishes,

Rebeca García Fandiño
Parc Cientific de Barcelona

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