AMBER Archive (2009)

Subject: Re: [AMBER] Polarizable simulation of the slab

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Nov 27 2009 - 10:10:38 CST

On Fri, Nov 27, 2009, Jan Heyda wrote:

> 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.

The nonbonded list code in sander assumes that the density of atoms in all
regions will be approximately homogeneous. It uses this assumption to
approximately divide work (and memory for data structures) among processors
in multi-CPU simulations. So, the code will indeed work on a single CPU, but
will find allocation failures in multiple-CPU runs.

I don't know the code well enough to estimate how hard it would be to fix
this. As it stands, what you want to do (parallel runs of polarizable
potential in a system where part is in vacuum) is outside the capabilities
of the code.

...regards...dac

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