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

[David]

-------- Forwarded Message --------
From: leafyoung81-group at yahoo.com
Reply-To: leafyoung81-group at yahoo.com
To: David <spoel at xray.bmc.uu.se>
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.
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?

Yang Ye

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

> On Tue, 2005-08-02 at 09:27 -0700,
> leafyoung81-group at yahoo.com wrote:
> > Hi, David
> > 
> > >From the dump file, I could only find that
> > 
> >    functype[0]=LJ_SR, c6= 1.24394384e-04, c12=
> > 1.14147088e-05
> if the atomtype for your dummy is 0 then they do
> have interactions.
> (Atomtype is determined by ther order in which atoms
> with non-zero LJ
> are found in the topology)
> >    ...
> > 
> > What other information can be referred to
> determine LJ
> > interaction between exactly two atoms?
> > 
> > Yang Ye
> > 
> > --- David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
> > 
> > > On Tue, 2005-08-02 at 11:39 +0800, Mu Yuguang
> (Dr)
> > > wrote:
> > > > Dear gromacs users,
> > > > We find that the dummy atoms do not have vdw
> > > interaction with other
> > > > atoms, even though we assign vdw parameters to
> the
> > > dummy atom type.
> > > > Is it a normal setting up in gromacs?
> > > No, did you run gmxdump to check your tpr file?
> > > 
> > > > Yuguang
> > > >
> _______________________________________________
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> http://www.gromacs.org/mailman/listinfo/gmx-users
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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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> > 
> > _______________________________________________
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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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> 
> 
-- 
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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