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

Berk Hess hess at kth.se
Fri Feb 14 14:31:50 CET 2020


In general one can not uniquely define a dipole in a periodic system. 
One can only define it when all molecules have no net charge. grompp 
warns about this when using the surface correction for PME.



On 2020-02-14 14:22 , David van der Spoel wrote:
> 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?

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