Tutorial-l Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Apr 25 2013 - 13:27:02 CDT

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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