[gmx-users] rigid linear molecules

[Christoph Freudenberger]

Lanyuan Lu wrote:
> I see the point now. But I'm still wondering that whether this method is 
 > widerly used by others in literature. I mean, can I use this directly to
 > write a paper ( which reference should I cite? ) or need I do a lot of
 > test first to justfy the model?

I also wonderer about this point already.
In all papers I have read about solvent models and small molecule
simulations this point has accually not been treated very broadly.
Usally the model is discribed with a single phrase like:
"A simple rigid model for xxx has been used"
Followed by some details about geometry, charges and LJ paramters,
but no details about HOW the model is kept rigid (besides that
maybe SHAKE has been used) but I never found any details about
angle constraints or improper dihedrals.

Is this common practice?

regards
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785