[gmx-users] resonance in ionised groups

[Anton Feenstra]

Luciane V. Mello wrote:

> Dear all
> 
> How do people generally cope with resonance in ionised groups?  If I
> wish to simulate a carboxylate at pH7, for example, how to know the
> correct bond length for the C-O bonds, something intermediate between
> C=O and C-O(minus)?  I also want to work with a phosphate group.  Then
> it seems even harder because of the hydrogen issue- how to average
> between P=O, P-OH and P-O(minus)?

The short answer is, we don't. Don't cope with, and don't know either.

The long answer is that the forcefields are parameterized to reproduce
certain experimental data (e.g., thermodynamic properties in case of the
Gromos, G34A*, forcefields), and will somehow include an average
discription of these group's behaviour because of that. That also means
that, in principle, the pH in your simulation is that at against which
your forcefield was parameterized (for which you can assume 7).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
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