Calculations on isolated molecules
ilya
Hello!
I wanted to clarify where should I place the molecule in the supercell
to make single molecule calculations. For example if I specify the CELL
%ABC 10.0 10.0 10.0, should I place the molecule at the origin or in
5.0 5.0 5.0? I also should set CELL%PERIODIC NONE and POISSON%PERIODIC
NONE. What value of POISSON%POISSON_SOLVER is most suited for
calculations on isolated molecules (the default is PERIODIC)?
Thanks a lot.
Ilya.
Teodoro Laino
the question depends of course on the poisson_solver (PS) you decide
to use. Specifically:
-) Martyna-Tuckermann (MT) PS is fully translational invariant.. This
means that the molecule can
be everywhere.
-) Wavelet (W) requires that the molecule is centered in the middle
of the box (use SUBSYS%TOPOLOGY%CENTER_COORDINATES
to achieve this purpose)
-) Multipole, is translational invariant
Which one is the best? As usual there's not a real best one..
Keep in mind that MT requires a simulation box at least double the
size of your system while W requires a box just slightly larger than the
size of the system (i.e. the density must be negligible at the border
of the simulation box, usually 3-4 Angstrom per side should be
enough.. but
again this depends on your basis set.. element.. simulation system).
While W could be more convenient because of the smaller cell size, MT
is undoubtedly more robust during an MD.. In fact is quite likely that
your system will start moving during an MD and if it's reaching the
border of the simulation box you will need to stop and restart the
calculation
(quite annoying though)..
Multipole is somehow something that lies in between.. requires that
density is small at the box boundaries but is translational
invariant. The main
problem of the multipole is that it is based on a fit.. therefore you
may have numerical problems and not fully an analytical cancellation
of the
periodic interactions..
Now.. the choice as usual is yours!
Teo