[gmx-users] Re: How the pressure is computed

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 14 15:29:06 CET 2012

Andrew DeYoung wrote:
> Justin, thank you very much for your time and help.  I am using pbc = xy
> (with two walls, one on each side), but my box actually expands wildly,
> which is very strange, rather than contracting and compressing the vacuum
> regions.  So I am not sure what to think.  Maybe I should switch to pbc =
> xyz and see what happens with the box size under NPT.  

I suspect it will collapse.  I don't know enough about what you're trying to 
achieve to make any real suggestions at this point.  I am also not familiar with 
the use of walls, though from your original post it seemed like you were trying 
to achieve an infinite system in z, which does not occur when using walls, per 
the manual.

> If you have time, I have another, related question.  I assume that the
> density stored in the .edr file (and printed using g_energy) takes into
> account the entire box volume, not just the part of the box which is not
> vacuum.  Is there any way to compute the density locally, i.e. in the part
> of the box actually occupied by molecules?

I doubt it.  The entire box volume is considered, as far as I know.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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