Hi Jesper –

 

Yes, a uniform dielectric is a pretty typical assumption for these kinds of calculations.

 

Thanks,

 

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997

http://nabaker.me

 

From: Jesper Sørensen [mailto:jesorensen@ucsd.edu]
Sent: Friday, May 25, 2012 11:58 AM
To: Baker, Nathan
Cc: apbs-users@googlegroups.com; (apbs-users@lists.sourceforge.net)
Subject: Re: [apbs-users] Manual calculation

 

And so I am assuming that in the dry calculations, that the eps(in) and eps(ext) are equal, correct? In other words using a uniform dielectric constant.

 

Best,

Jesper

 

 

On May 24, 2012, at 6:40 PM, Baker, Nathan wrote:



Hello –

 

You should use the same surface definition (surface type and probe radius) for all steps of the calculation.  However, if the internal and external dielectric values are equal in some parts of the calculation, then the surface won’t actually be calculated for those parts of the calculation.

 

Thanks,

 

__________________________________________________ 
Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997
http://nabaker.me

 

From: apbs-users@googlegroups.com [mailto:apbs-users@googlegroups.com] On Behalf Of Jesper Soerensen
Sent: Wednesday, May 23, 2012 1:48 PM
To: apbs-users@googlegroups.com
Subject: [apbs-users] Manual calculation

 

Dear all,

 

I am running a manual (mg-manual) calculation with the SE surface.

3 calculations are solvated and 3 are dry like shown in the APBS examples and according to the thermodynamic cycle.

 

My question is, in the dry set of calculations, should the 'srad' still be 1.4 like in the solvated calculations?

I mean because in the absence of solvent does it make sense to define the SE surface? But at the same time changing it, results in two different surfaces being used and therefore some terms may not cancel out?

 

I hope you can provide some insight.

 

Best regards,

Jesper

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