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Hello,
I'm trying to calculate the electrostatic energy between two nucleosomes in
a dinucleosome complex using apbs, and I'm having problems converging the
calculation 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 internucleosome electrostatic energy
(dinucleosome - nucleosome1 - nucleosome2) is not well converged and gives
very large values. For instance, it changes from -341 kJ/mol for 0.5A to
-563 kJ/mol for 0.35 A. (No evident errors 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 procedure and prize.py to calculate the dimensions of the sub
grids, and then summed the energies for each calculation. A new problem is
that when I split the calculation I start getting warning messages for the
subgrid calculations (Unusually large potential values detected on the
focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations!).
Furthermore, the resulting energy (direct sum of the energies given by each
of the subgrid calculations) seems to diverge now, it is -1740 kJ/mol for 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 systems and if
you could give me a few hints as to what I could do in order to converge
this calculation.
With thanks and best wishes,
Rosana
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Hello,

I'm trying to calculate the electrostatic energy between =
two nucleosomes in a dinucleosome complex using apbs, and I'm having proble=
ms converging the calculation against grid size.

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

=

For those grid spacings the resulting intern=
ucleosome electrostatic energy (dinucleosome - nucleosome1 - nucleosome2) i=
s not well converged and gives very large values. For instance, it changes =
from -341 kJ/mol for 0.5A to -563 kJ/mol for 0.35 A. (No evident=
errors or warning messages are reported by apbs)

The problem is that if I further decrease the grid spacing, I ne=
ed to split the calculation as explained in the apbs website. I used the&nb=
sp;asynchronous parallel procedure and prize.py to calculate the dimensions=
of the sub grids, and then summed the energies for each calculation. =
A new problem is that when I split the calculation I start getting warning =
messages for the subgrid calculations (Unusually large potential values&nbs=
p;detected on the focusing boundary! Convergence not guaranteed for NP=
BE/NRPBE calculations!).

Furthermore, t=
he resulting energy (direct sum of the energies given by each of the subgri=
d calculations) seems to diverge now, it is -1740 kJ/mol for a grid spacing=
of 0.2A and to -3697 kJ/mol for a grid spacing of 0.15A. I also tried chan=
ging ofrac, but without any noticeable improvement.

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

With thanks and best wishes,

Rosana

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