[gmx-users] what's the meaning of pbc=no?
wangzhun at pumc.edu.cn
Mon Nov 14 07:04:11 CET 2005
Could you provide some details on setting the potential?
I can not find relevant information in the mannual.
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 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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