[gmx-developers] box distortion with isotropic pressure coupling

Chris Neale chris.neale at utoronto.ca
Mon Jul 21 21:36:20 CEST 2008

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:

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:  

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:

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,

More information about the gromacs.org_gmx-developers mailing list