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

Stéphane Téletchéa stephane.teletchea at jouy.inra.fr
Thu Mar 6 13:57:31 CET 2008

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?

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).

Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

More information about the gromacs.org_gmx-users mailing list