[gmx-users] problems with barostats-thermostats

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 20 21:07:00 CET 2006

Argyrios Karatrantos wrote:
> Hi
> i am doing an NPT simulation of Argon (LJ fluid). whenever i set up the 
> temperature and pressure with Berendsen algorithm everything works fine, 
> but when i use Nose-Hoover for temperature (taut=0.1 or 0.01) and 
> Parrinelo Rahman for pressure (taup=0.1 or 0.01) the simulation crashes 
> a little before the end,the   run is killed by signal 12 (USR2) or 
> signal 11 (SEGV). does anyone have any idea what is the problem so  the 
> simulation is killed by those signals?
Check your output!

You probably have large fluctuations in P and/or T. See GROMACS article 
in JCC 2005 for more info.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list