Hi Matthew –

 

If there are no other errors, you should be fine.  However, it might be worthwhile to test the sensitivity of your results to the fglen parameters.

 

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://kdi.pnl.gov/bios/baker.stm

 

From: Matthew Adendorff [mailto:mattadendorff@gmail.com]
Sent: Sunday, October 23, 2011 7:12 PM
To: Baker, Nathan
Subject: Re: [apbs-users] DNA Focusing Boundary Problem

 

Hi,

 

There are no errors or warnings in the output besides this one. 

 

Many thanks,

 

Matthew

On Sun, Oct 23, 2011 at 9:49 PM, Baker, Nathan <Nathan.Baker@pnnl.gov> wrote:

Hello –

 

This isn’t an error, just a warning.  Did you see any other warnings or errors in the output?

 

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://kdi.pnl.gov/bios/baker.stm

 

From: Matthew Adendorff [mailto:mattadendorff@gmail.com]
Sent: Sunday, October 23, 2011 10:20 AM
To: apbs-users@lists.sourceforge.net
Subject: [apbs-users] DNA Focusing Boundary Problem

 

Good day,

 

I have been using APBS for electrostatic calculations on long DNA helices interacting with one another. Recently when I ran a single 120 bp helix the solver returned the following error: 

 

focusFillBound:  WARNING! Unusually large potential values
                   detected on the focusing boundary!  
                   Convergence not guaranteed for NPBE/NRPBE calculations!

 

These DNA helices usually have a predominantly negative surface (at lower salt concentrations), however these results show a large positive region in the middle of the structure. I was wondering how I should proceed to try and alleviate this error?

 

Many thanks,

 

Matthew