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!).
Regards,
Pablo
--
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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
