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

[David van der Spoel]

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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