Chemistry Reference
In-Depth Information
complexes. Also time-dependent diffusional processes (below). Available:
http://apbs.sourceforge.net/.
UHBD: Solves the linearized or nonlinear PB equation. Available: http://
mccammon.ucsd.edu/uhbd.html.
Charmm PB: APBS codes utilized in the CHARMM package. Available:
http://biowulf.nih.gov/apps/charmm/charmmdoc/c33b2/apbs.html, or
FD approach http://biowulf.nih.gov/apps/charmm/charmmdoc/c33b2/
pbeq.html.
DelPhi: Code to solve the linearized PB equation. Available: http://wiki.
c2b2.columbia.edu/honiglab_public/index.php/Main_Page.
PME in AMBER: Sagui's group has contributed MG solvers to the PME
forcefields. Available: http://amber.scripps.edu/.
Transport
APBS (above): Models for ion and large biomolecule transport.
PNP solver: Beck group MG-PNP solver for ion transport is freely
available on request. Contact thomas.beck@uc.edu.
TranSIESTA: General-purpose electronic structure code (above),
adapted to electron transport calculations.
MIKA: General-purpose real-space electronic structure code (above),
adapted to electron transport calculations.
octopus
: Real-space electronic structure code (above) with emphasis
on TDDFT and electron transport codes planned.
This list is not complete, but it should provide a good entry into available soft-
ware for real-space calculations. It is interesting to note that the real-space
field has gone from a few developmental studies to a wide range of relatively
mature codes in about 15 years.
SOME SPECULATIONS ON THE FUTURE
This last section presents a few speculations on research directions that
may be pursued in the future.
Chemistry and Physics: When Shall the Twain Meet?
Chemists are steeped in the tradition of wave functions and basis set cal-
culations.
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This mindset has come about mainly because the wave function/
orbital picture has been extremely helpful in the development of chemical
ideas. Physicists, on the other hand, have traditionally focused on periodic
