[Fwd: Re: [gmx-users] dummy atom vdw interactions]

[leafyoung81-group at yahoo.com]

Yes. Dummy atoms also have vdw calculations. I was
drawing the wrong conclusion because of exclusion.

--- David <spoel at xray.bmc.uu.se> wrote:

> On Wed, 2005-08-03 at 00:41 -0700,
> leafyoung81-group at yahoo.com wrote:
> > 
> > --- David <spoel at xray.bmc.uu.se> wrote:
> > 
> > > 
> > > > Subject: Re: [gmx-users] dummy atom vdw
> > > interactions
> > > > Date: Wed, 3 Aug 2005 00:05:48 -0700 (PDT)
> > > > You are right, David. For a system of two
> types of
> > > > atom (one 'real' and one 'dummy', with
> different
> > > sigma
> > > > and epsilon), there are four types of
> functype.
> > > 
> > > Do you find four different LJ parameters in the
> tpr
> > > file then?
> > Yes. From dump file of tpr, there are four types
> of
> > LJ.
> Then show us the parameters and explain what you
> mean with no repulsion.
> 
> > > 
> > > > However, from the simulation, putting one
> dummy
> > > and
> > > > one real together, there is no replusion. May
> I
> > > know
> > > > where the source code dealing with vdw and
> dummy
> > > is?
> > > Check grompp.c
> > > 
> > > > 
> > > > Yang Ye
> > > > 
> > > 
> > > -- 
> > > David.
> > >
> >
>
________________________________________________________________________
> > > David van der Spoel, PhD, Assoc. Prof.,
> Molecular
> > > Biophysics group,
> > > Dept. of Cell and Molecular Biology, Uppsala
> > > University.
> > > 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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> > > 
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> -- 
> David.
>
________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular
> Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> 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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> 
>