[DFTB-Plus-User] N-H skf files

Bálint Aradi aradi at uni-bremen.de
Tue Mar 21 14:50:21 CET 2017

Dear Lin,

> I’m confused which N-H skf file should I use, the mio-1-1 set or the 
> miomod:nh set? My system is an enzyme and I’m using DFTB as the
> quantum method to do QM/MM MD studies in AMBER. Under the miomod:nh
> page, I found that it is modified to reproduce the sp3 nitrogen and
> proton affinity better, but the spa nitrogen are descibed correctly
> by the original mio-1-1 set. Now my system has both sp2 and sp3
> nitrogen, should I use the original mio-1-1 set or the modified
> miomod:nh set? I appreciate any help!

I am not really an expert on those systems and never used those
'improved' modified interactions, so be critical about any advice I give
below. Probably, you should try to contact the SK-file authors directly...

But anyway, I guess, you have two options. You could use the original
mio-1-1 for all elements and check results on small relevant systems
against ab initio. If it is not satisfying at all, you could introduce
two type of nitrogens in your system, one for the sp2 and one for the
sp3 configuration and use the different Sk-files for them. On the
SK-file level, that is somewhat messy, you would have create all
interacations of the second N type (let's call it N2) with all other
elements (including the original N). For most interaction, you just copy
and rename the original interactions, while for N-H and H-N you would
take it from the modified set.

Best regards,


Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen

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