I started from equilibrated NPT simulation, which gave box with
dimensions approximately 32A x 32A x 32A.
System was then shifted by 75A in z-coordinate (by awk) and z-PBC
changed to 150, so the final system sizes were 32A x 32A x 150A, and all
atoms were in the z-region 59A-91A.
The system was thou inhomogeneous in total, but in fact it's 60A of
vacuum, 32A of water, and 60A of vacuum. This should be stabile during
simulation.
Jan
> ------------ Původní zpráva ------------
> Od: case <case.biomaps.rutgers.edu>
> Předmět: Re: [AMBER] Polarizable simulation of the slab
> Datum: 27.11.2009 15:37:54
> ----------------------------------------
> On Thu, Nov 26, 2009, Jan Heyda wrote:
> >
> > I'm dealing with slab calculation - so NVT calculation, in which the
> > polarizable force field has to be used. The system consists of about
> > 1000 water molecules and few ions. The system size should therefore be
> > something like 32A x 32A x 150A.
>
> Can you define what you mean by "slab"? How is it different that "bulk"?
> Do you in fact have a uniform density of atoms in the system?
>
> ...dac
>
>
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Received on Fri Nov 27 2009 - 07:00:04 PST
