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From: Houyang Chen (houyangchen2008_at_hotmail.com)
Date: Thu Apr 25 2013 - 13:43:03 CDT

Hi James,
I see. Thanks
Houyang


Subject: Re: tutorial-l: a question regarding eField calculation
From: gumbart_at_ks.uiuc.edu
Date: Thu, 25 Apr 2013 14:27:02 -0400
CC: tutorial-l_at_ks.uiuc.edu
To: houyangchen2008_at_hotmail.com

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:
http://www.sciencedirect.com/science/article/pii/S0005273611003361

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?

Thanks.
Houyang

                                               
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