[gmx-users] rigid linear molecules

[Anton Feenstra]

Christoph Freudenberger wrote:
> 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.

A 'simple rigid model' could be constructed in various ways, but not
using the usual SHAKE implementations that only constrain distances.
If it really is simple & rigid, it should need no further explanation.
Aren't there methodological papers on this, e.g. in jcc?

By the way, if you're going to write this down, don't call them 'dummy
atoms' the way I did that in my paper on 'dummy hydrogens'. I later
realized that the term 'dummy atoms' is already used in various
different contexts. I'd suggest 'interaction points', since that is what
they actually are: a point in space (defined from other atoms), where the
interactions of a 'chemical' atom (LJ & Coul) reside.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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