[gmx-users] Improper dihedrals on planar rings

Pablo Englebienne p.englebienne at tue.nl
Thu Oct 15 14:37:01 CEST 2009

Hi all,

I have a question about the setting of improper dihedrals. I have a 
pyrimidinone I want to use with the G53a5 force field, but I can't get 
the ring to stay flat.

First question is: do all atoms in the planar ring need to have 3 
subsituents? I.e., should an explicit atom of type HC be present on the 
CHs within the ring, or could they be united atoms (e.g., non-bonded 
type CR1)?

Second question: how many parameters are required to keep the ring 
planar? I initially though that each bond within the ring should have an 
improper torsion defined, with the bonds in the J-K atoms in the 
torsion. In addition, every center bound to 3 other atoms (e.g., C=O, 
N-H) needs an additional term, with the central atom as atom I. If all 
atoms have 3 substituents, this would mean 6 bonds + 6 centers = 12 
improper torsions. Is that the minimum number of improper torsions 
required to keep a 6-membered ring flat? What about a 6-membered ring 
represented with united atoms?

Thanks for reading so far (and many thanks for replying!).



Pablo Englebienne, PhD
Institute of Complex Molecular Systems (ICMS)
Eindhoven University of Technology, TU/e
PO Box 513, HG -1.26
5600 MB Eindhoven, The Netherlands
Tel +31 40 247 5349

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