[gmx-developers] Storing the system dipole for predicting infrared spectra

[David van der Spoel]

Hi,

it would be useful to be able to store the system dipole for whole 
molecules from an MD simulation for computing infrared spectra. It seems 
that the dipole that is calculated when using the PME surface correction 
is based on broken molecules (but that may be correct for that purpose).

I have implemented an "applied force" that acts to store the (still 
incorrect) dipole and then writes it to a file at the end of the run.

However, I wonder whether it would be better to have the option to store 
the dipole in the energy file again (with a warning that it will slow 
down the simulation)?

Any clues?
-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se