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

Wang Zhun 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.
> ________________________________________________________________________
> 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.

More information about the gromacs.org_gmx-users mailing list