Thanks for your reply. I will try =
these suggestions, and will post here the results if I succeed. I actually =
want to compare this binding energy between a set of systems with different=
mutations and conformations, and was trying to find the best settings in o=
ne example first. So, at the end I will be computing relative energies. One=
more question, for these comparisons, all the calculations should be done =
exactly on the same grids, not only grid spacings, but also dimensions and =
centers, right?

Thanks,

Rosana

On Friday, May 10, 2013 12:27:45 AM UTC+2, Baker, Nathan wrote:

Hi= Rosana =E2=80=93

This = is a warning message intended to encourage you to explore the sensitivity o= f your results to the calculation parameters. In your case, I would r= ecommend varying the =E2=80=9Cpdime=E2=80=9D (increase it) and =E2=80=9Cofr= ac=E2=80=9D (increase it) parameters to see how much they influence your re= sults.

However, I would= also encourage you to clarify the problem you=E2=80=99re solving with APBS= . Absolute electrostatic binding energies aren=E2=80=99t usually very= meaningful =E2=80=93 quite often you=E2=80=99re more interested in relativ= e values of binding energies as differences calculated when testing multipl= e mutations, solution conditions, titration states, etc. It is likely= that these relative energies are more stable with respect to grid setup (w= ithin reason).

=

Thanks,<= /span>

--

Nathan Baker

Pacific Northwest National Labora= tory

+1-509-375= -3997

<= p class=3D"MsoNormal">**From:** Rosana Collepard=
o [mailto:r.coll...@gmail.com**Sent:** Thursday, =
May 09, 2013 2:56 AM**To:** apbs-...@googlegroups.com

<=
b>Subject: [apbs-users] Convergence problems in very large calculation<=
/span>

Hello,

= I'm tr= ying to calculate the electrostatic energy between two nucleosomes in a din= ucleosome complex using apbs, and I'm having problems converging the calcul= ation against grid size.

The calculation requires a lot of memory, = but using fine grid spacings of 0.5 and 0.35 A requires less than the = ~28GB apbs limit.

=

For those grid spacings the resulting internucl= eosome electrostatic energy (dinucleosome - nucleosome1 - nucleosome2) is n= ot well converged and gives very large values. For instance, it changes fro= m -341 kJ/mol for 0.5A to -563 kJ/mol for 0.35 A. (No evident er= rors or warning messages are reported by apbs)

The problem is that = if I further decrease the grid spacing, I need to split the calculation as = explained in the apbs website. I used the asynchronous parallel proced= ure and prize.py to calculate the dimensions of the sub grids, and the= n summed the energies for each calculation. A new problem is that when I sp= lit the calculation I start getting warning messages for the subgrid calcul= ations (Unusually large potential values detected on the focusing boun= dary! Convergence not guaranteed for NPBE/NRPBE calculations!).=

Furthermore, the resulting energy (direct sum of the energies given by ea= ch of the subgrid calculations) seems to diverge now, it is -1740 kJ/mol fo= r a grid spacing of 0.2A and to -3697 kJ/mol for a grid spacing of 0.15A. I= also tried changing ofrac, but without any noticeable improvement.

I wanted to know if anyone has experience with very large syste= ms and if you could give me a few hints as to what I could do in order to c= onverge this calculation.

With thanks and best wishes,

Rosana