[gmx-users] distance between oxygens of hydroxils in the OPLS

Milton Taidi Sonoda msonoda at iqm.unicamp.br
Mon Jan 26 18:07:01 CET 2004

I have tested a simulation of a single ethanediol in a
periodic box, with the starting configuration appropriate
for an internal H bond formation, and everything were fine.
The oxygens remained far apart, and the hydroxils bond streaching
were well-behaved.
I don't know what is going on with the carbohydrate simulation.

Milton Taidi Sonoda wrote:

> Hi all
> I'm having problems with oxygens of diferent hydroxils of
> a carbohydrate molecule. I'm using OPLS forcefield and
> this oxygens are 1-4 bonded neighbor. They are aproaching
> at distances as close as 0.12 nm from eachother, however their
> vdw sigma parameter are 0.307 nm. Distances like this makes
> the hydrogen of the hydroxil ill-behaved.
> Does anyone have advice to give?
> Thank you in advance.
> Milton Taidi Sonoda
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