[gmx-users] rigid linear molecules
David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 18 15:20:01 CEST 2003
On Thu, 2003-09-18 at 14:57, 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?
> Thanks for all kind help.
Yes you can. This is fully accepted, there are quite a few papers using
this, see gromacs manual for some refs. Of course you need to justify
the model in terms of normal properties such as energy, density etc.
> Lanyuan Lu
> ----- Original Message -----
> From: "Christoph Freudenberger" <christoph.freudenberger at chemie.uni-ulm.de>
> To: <gmx-users at gromacs.org>
> Sent: Thursday, September 18, 2003 7:39 AM
> Subject: Re: [gmx-users] rigid linear molecules
> > Anton Feenstra wrote:
> > > lulanyuan wrote:
> > >
> > >> Thanks for reply. But after reading the whole discussion of
> > >> acetonitril, I found that to ajust the moment
> > >> of inertia, I have to change the bond length. I think this totally
> > >> changed the model and will affect the other
> > >> parameters in the model(charges and LJ).
> > >> Does anyone do things like this kind of mass redistribution in
> > >> literature? Can anyone
> > >> give me some reference for this kind of dummy use?
> > >
> > >
> > > You missed the point. The trick is to creat two masses (i.e. atoms without
> > > charge and LJ parameters, so without any interactions), at the appropriate
> > > distance (use a constraint) to reproduce moment of inertia. Then, use the
> > > dummy atom constructions (see manual), to create three 'dummy' atoms at the
> > > approprate relative positions, these 'dummies' are your 'real' C and O
> > > atoms,
> > > and are the sites of the LJ and Coulomb interactions (and have no mass).
> > >
> > > It would look a little like this:
> > >
> > > O--M-----C-----M--O
> > Hi lulanyuan,
> > It was me, who started the disscusion about rigid models for linear
> > molecules some time ago and I managed to create a topology for
> > acetonitrile with the help of David, Anton and some others.
> > You can download this topology from the molecules site and use
> > it as a template for CO2.
> > regards
> > --
> > Christoph Freudenberger
> > Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
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Dr. David van der Spoel, Dept. of Cell & Mol. 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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