[gmx-users] resonance in ionised groups

[Luciane V. Mello]

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)?

Thanks in advance for your help

Luciane