[gmx-users] Skewed box using Parrinello-Rahman pressure coupling

Berk Hess gmx3 at hotmail.com
Fri Mar 7 10:14:00 CET 2008

> Date: Thu, 6 Mar 2008 13:57:31 +0100
> From: stephane.teletchea at jouy.inra.fr
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling
> Berk Hess a écrit :
> > Hi,
> > 
> > I now realized that my fix what completely incorrect.
> > I wanted to multiply the margin of 0.0001 by 2, not the factor 0.5.
> > But my mistake means that is now given an error when the off diagonal
> > element is relatively more than 1 instead of more than 0.5.
> > This is a far too weak check.
> > So I would not expect any fatal errors any more with this incorrect check.
> > Therefore I don't understand why you still get errors.
> > 
> > Could you try changing BOX_MARGIN to 0.5005, as it currently is in 
> > version 4.0?
> > 
> > Berk. 
> We thus need a hot fix for 3.3.3?

A too weak check does, by itself, not cause problems.
It does mean that the check is useless, but Gromacs
by itself never generates incorrect boxes.

The problem with the check is still there, but it only
seem to occur very rarely.
I'll fix it properly in the CVS 3.3 patches branch.

> To Luther:
> Do you have by any hazard
> constraints                = all-bonds
> if so, could you check if the run has the error with h-bonds?
> In my case that solved the issued with the error message. I suspect a 
> rounding problem but i have not figured out it yet (not really searched 
> for, btw).

I don't think this should have anything to do with the problem directly.
Indirectly it could help, but only when the system is unstable.


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