[gmx-users] Hydrogens moving inside ring?

[Anton Feenstra]

Joanna Bailey wrote:
> I am running a molecule which includes a triazine ring, where two of the 
> nitrogens have hydrogens and two of the carbons are part of carbonyl 
> groups.  When I run the energy minimisation, which converges, the 
> hydrogens end up inside the ring with the ring remaining flat. Obviously 
> there is something very wrong, I have checked the dihedrals both 
> improper and proper and the bond angles, all seems fine. Is there 
> anything else anyone could suggest could be the problem? Thank you.

Have you considered that for dihedrals (propers as well as impropers),
'cis' is zero?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|