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

David van der Spoel spoel at xray.bmc.uu.se
Fri Feb 14 14:43:41 CET 2020

Den 2020-02-14 kl. 14:31, skrev Berk Hess:
> Hi,
> 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.

That is correct, but it does not answer my question. This is of course 
relevant to liquids mainly.

It could also be used for storing the electric current in a simulation 
without saving the velocities at every time step (and this also works 
for charged systems).

> Cheers,
> Berk
> 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?

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.

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