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

[David]

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
> >
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the
> > list. Use the 
> > www interface or send it to
> > gmx-users-request at gromacs.org.
> > 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++