[gmx-users] what's the meaning of pbc=no?
g0403186 at nus.edu.sg
Mon Nov 14 05:40:45 CET 2005
It's really a good idea.
Thanks very much
----- Original Message -----
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: "Dai Liang" <g0403186 at nus.edu.sg>; "Discussion list for GROMACS users"
<gmx-users at gromacs.org>
Sent: Monday, November 14, 2005 2:26 AM
Subject: Re: [gmx-users] what's the meaning of pbc=no?
> 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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