[gmx-users] rigid linear molecules

[David]

On Fri, 2003-09-19 at 19:09, lulanyuan wrote:
> You can't do it that way. Shake won't work for this kind of
> three atom linear molecule. You can see some testbook of MD for
> details, such as "Computer Simulation of Liquids".

the reason is simply that shake only exerts a correction along the bond.
if your central atom  moves off the straight line shake will never
converge.

> Lanyuan Lu
> 
> ----- Original Message -----
> From:"Gianfranco Bocchinfuso" <gianfranco.bocchinfuso at uniroma2.it>
> To:<gmx-users at gromacs.org>
> Subject:Re: [gmx-users] rigid linear molecules
> Date:Fri, 19 Sep 2003 23:00:20 +0800
>  >----- 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
>  >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.
>  >
>  >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.
>  >>
>  >>
>  >> --
>  >> Groetjes,
>  >>
>  >> Anton
>  >>   _____________ _______________________________________________________
>  >> |             |                                                       |
>  >> |  _   _  ___,| 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/       |
>  >> |             | "If You See Me Getting High, Knock Me Down"           |
>  >> |             | (Red Hot Chili Peppers)                               |
>  >> |_____________|_______________________________________________________|
>  >>
>  >>
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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