[gmx-users] what's the meaning of pbc=no?

[David van der Spoel]

On Mon, 2005-11-14 at 14:04 +0800, Wang Zhun wrote:
> Could you provide some details on setting the potential? 
> I can not find relevant information in the mannual.
You mean for the wall?

Just generate the coordinates using a small script and make it Argon
like atoms with strong lennard jones.
> 
> Thanks!
> 
> 
> In your mail:
> >From: David van der Spoel <spoel at xray.bmc.uu.se>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: Dai Liang <g0403186 at nus.edu.sg>,
> Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] what's the meaning of pbc=no?
> >Date:Sun, 13 Nov 2005 19:26:51 +0100 (CET)
> >
> >On Sun, 13 Nov 2005, Dai Liang wrote:
> > 
> > >I want to do a simulation without periodic boundary condition, but I am confused by the meaning of pbc=no.
> > >It may have two meanings. 
> > >First, no box, then liquid water becomes vapour because pressure is zero.
> > >Second, there is a box. any atom who collides the box will be reflexed. but here no image box.
> > >
> > 
> > >The simulation I intend to do is the second one, but gromacs seems to do the first one.
> > That's correct.
> > You can model a rigid wall of LJ particles if you want reflections, then 
> > you have to embed that in vacuum to avoid interactions accross the walls.
> > >
> > >who can clarify it? thanks
> > 
> > -- 
> > 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++