[gmx-users] rigid linear molecules
gianfranco.bocchinfuso at uniroma2.it
Fri Sep 19 17:01:02 CEST 2003
----- Original Message -----
From: "Anton Feenstra" <feenstra at chem.vu.nl>
To: <gmx-users at gromacs.org>
Sent: Friday, September 19, 2003 8:23 AM
Subject: Re: [gmx-users] rigid linear molecules
> Christoph Freudenberger wrote:
> > Lanyuan Lu wrote:
> > > I see the point now. But I'm still wondering that whether this method
> > > widerly used by others in literature. I mean, can I use this directly
> > > write a paper ( which reference should I cite? ) or need I do a lot
> > > 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.
if I have a linear molecule A--B--C what is the problem if I use shake to
constrain the bonds A-B, B-C and A-C? I think that the 3rd constrain make
the molecule linear, or not?
> 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.
> _____________ _______________________________________________________
> | | |
> | _ _ ___,| K. Anton Feenstra |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
> | | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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