[gmx-users] box size changing during isotropic pressure coupling

Berk Hess gmx3 at hotmail.com
Thu Jul 24 21:11:41 CEST 2008


The triclinic case shows a systematic looking difference between x/y and z.
But here x and y are really identical, so they will always stay identical.
The magnitude of the effect is very small though.
I would not worry about it.

I don't think it is worth putting more effort into, since it has been fixed for 4.0.


> Date: Thu, 24 Jul 2008 14:55:24 -0400
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] box size changing during isotropic pressure coupling
> >Here tau_p=4, which is already quite large.
> >But there are no "real" problems in the system, the results should be fine.
> >But the relative ling tau_p might be the reason for the strange scaling.
> >This would make the scaling factor always close to 1 plus or minus one bit.
> >I have not done the binary math, so I can not see if somehow this would
> >make numbers slightly below 20 scale down and above 20 scale up.
> While this makes some sense, the triclinic box data that I have posted 
> http://www.pomeslab.com/CN_GromacsPost_071808.html (bottom of page)
> suggests that there is no such split at 20 nm but that this may be more of an X+Y vs Z issue.
> David mentioned that the website was not available? Sorry, it does appear to be visible now though.
> Please let me know if you can not see the images and I will post them to photobucket or some such site.
> Thanks again,
> Chris.
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