From: Houyang Chen (
Date: Thu Apr 25 2013 - 13:43:03 CDT

Hi James,
I see. Thanks

Subject: Re: tutorial-l: a question regarding eField calculation
Date: Thu, 25 Apr 2013 14:27:02 -0400

Yes, you do include the whole box length to get dV (L_system + L_vacuum), although you should actually calculate the full potential in your system because you'll find that the dV across the non-vacuum part of your system is closer to E*L_system. Take a look at this paper for more insight:

FYI, almost no one reads tutorial-l, so you will get a better response on namd-l in the future.
On Apr 25, 2013, at 2:04 PM, Houyang Chen wrote:Dear all,
I have a question regarding eField calculation.
In page 31 of Bionanotechnology tutorial (Alek Aksimentiev, Jeffrey Comer, May 2007), the
relationship of voltage and electric field is given as
eFieldz/(kcal/mol.A.e)=-23.060549 (U/V)/(lz/A)
and the value of lz can be obtained from c_z of sample.xsc.

My question is that if I applied a vacuum gap at z-axis, how can I calculate the eFieldz?
Does the value of lz containing the width of vacuum gap in z-axis?


** Visit for more info on majordomo