[gmx-users] I know about improper dihedrals (i.e. gi_1) , etc. Is there a way to keep phenyl rings absolutely flat.

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 3 09:27:23 CEST 2010


Mind not to set force constants too high, as they will introduce high
frequency motions, high speeds, and decreased stability. Indeed,
absolute flatness need not be required. Phenyl rings naturally come
with out of plane motions. Is there reason to believe that the extent
of the deformations is too large, or is there a consistent



On Thu, Jun 3, 2010 at 9:02 AM,  <comcon1 at erg.biophys.msu.ru> wrote:
>> Hi, all,
>> I need to keep a molecule absolutely flat. I know about improper
>> dihedrals (i.e. gi_1), but it doesn't seem to be enough to keep it
>> flat.  It seems to get bent a little bit.  I have a system with a
>> phenyl ring and protons and I am trying to run GROMOS 96 ff53a6 force
>> field.  I appreciate your ideas.
> What is <<absolute flatness>>?? For instance you can set up very-very-very
> big thickness constant in the improper definition. But i didn't ever have
> such <<thickness>> problem with aromatic compounds.. Show us your itp and
> gro, please.
> comcon1,
> Biophysical department,
> Biology faculty,
> Moscow State University, Russia.
>> Much appreciated,
>> Art
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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