[gmx-users] dummy atom vdw interactions

[David]

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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> > -- 
> > 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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