[gmx-developers] box distortion with isotropic pressure coupling

Chris Neale chris.neale at utoronto.ca
Thu Jul 24 01:54:00 CEST 2008

I took a look at the cvs code and I wonder if the fix is simply the call 
to preserve_box_shape()
that has been added to void berendsen_pscale()?

While the method applied by preserve_box_shape() via do_box_rel() 
appears quite reasonable,
this still doesn't explain to me why there would be a problem without 
this fix, and, specifically,
why x and y would tend to decrease while z tends to increase in the 
absence of a call to

Any comments at all would be appreciated.

Chris Neale wrote:
> Dear developers,
> I have a 'rectangular' system and many rhombic dodecahedron systems 
> that, when simulated under
> isotropic pressure coupling, show a variable ratio of box side 
> lengths. This does not happen for
> cubic systems.
> I gather that this is a known bug, and that it has been fixed for 
> gromacs 4, but I would like to get some details about the exact nature 
> of this ex-bug in order to determine how valid my simulations are. I 
> suspect that it's something to do with using box_x*box_y as a divisor 
> somewhere for all planes in the pressure coupling, as that would 
> explain why there is no effect for cubic systems.
> I do not expect that there would be a serious problem for a protein in 
> a box of water, but I imagine that it is possible that isotropic 
> studies on detergent self-aggregation and especially semi-isotropic 
> studies of lipid bilayers could suffer from significant 
> non-equilibrium forces. This would be especially
> relevant for lipid bilayers now that it is fixed since some lipid 
> parameter refinement was conducted while using earlier versions of 
> gromacs and may now require re-investigation.
> I posted this on the users list:
> http://www.gromacs.org/pipermail/gmx-users/2008-July/035264.html
> When I mentioned this on the list, I was pointed to some
> bugzilla comments: http://bugzilla.gromacs.org/show_bug.cgi?id=165  
> that reference revision comments:  
> http://www.gromacs.org/gromacs/revisions/
> Berk Hess
> 13 Feb 2008
> box distortion with pressure coupling
> In all Gromacs versions before 4 the box shape would "diffuse" over  
> time when using (semi)isotropic pressure coupling. This issue (only  
> noticable for very long simulations) has been fixed for version 4.0.
> Which I then reposted to the users list:
> http://www.gromacs.org/pipermail/gmx-users/2008-July/035270.html
> If anybody knows the exact nature of the bug then I would be grateful 
> to hear about it
> and ideally to see some code snippits or a diff.
> Many Thanks,
> Chris.
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