[gmx-users] rigid linear molecules
lulanyuan at sina.com
Fri Sep 19 19:11:01 CEST 2003
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".
----- 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
>> > > 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/ |
>> | | "If You See Me Getting High, Knock Me Down" |
>> | | (Red Hot Chili Peppers) |
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