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

David van der Spoel spoel at xray.bmc.uu.se
Sun Nov 13 19:26:51 CET 2005

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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