AMBER: Electron density profile

From: <>
Date: Thu, 20 Dec 2007 13:13:56 +0100

Dear Amber users,

I am currently simulating a POPC membrane bilayer. In that regard, I
have read the following article:

Jójárt, Martinek: Performance of the General Amber Force Field in
Modeling Aqueous POPC Membrane Bilayers, Journal of Computational
Chemistry (2007)

To evaluate membrane bilayer thickness, computed electron density
profiles were compared to experimental profiles. As stated in the
article, "The electron density profiles were computed by using the
atom distribution data ensemble and time averaged for the last
nanosecond of simulations C, D and E."

I was wondering whether this can be accomplished in ptraj?

If not, are there any other suggestions as to how to evaluate membrane
bilayer thickness?

Thanks in advance.

Best regards,

Ĺge Skjevik
Department of Biomedicine
University of Bergen, Norway
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Received on Sun Dec 23 2007 - 06:07:16 PST
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