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.
Pacific Northwest National Laboratory
From: Matthew Adendorff [mailto:firstname.lastname@example.org]
Sent: Sunday, October 23, 2011 7:12 PM
To: Baker, Nathan
Subject: Re: [apbs-users] DNA Focusing Boundary Problem
There are no errors or warnings in the output besides this one.
On Sun, Oct 23, 2011 at 9:49 PM, Baker, Nathan <Nathan.Baker@pnnl.gov> wrote:
This isn’t an error, just a warning. Did you see any other warnings or errors in the output?
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?