[gmx-users] Mdrun box nan error

[Nathalie R. Basdevant]

David-
Thanks fir your reply. I am using 1ps for pressure coupling should I use a
larger constant .e.g 5-10ps?
-- 
Nathalie
> -----Original Message-----
> From: gmx-users-admin at gromacs.org 
> [mailto:gmx-users-admin at gromacs.org] On Behalf Of David
> Sent: Friday, May 07, 2004 2:50 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Mdrun box nan error
> 
> On Fri, 2004-05-07 at 18:21, Nathalie R. Basdevant wrote:
> > Dear users,
> > 
> > I am running Gromacs 3.2.1 on an itanium 2 with Linux compiled with 
> > Intel compilers. The system that I am simulating consists 
> of a protein 
> > in water box (OPLS+tip4p). I am simulating under NPT (both 
> Berendsen 
> > baths) 300K and 1atm. I am running in parallel (4 processors).
> > Every once in a while the simulation crashes with the 
> following error 
> > messages (see below). However when I restart the simulation 
> (tpbconv 
> > -f .trr -e .edr ) the simulation passes through the step that had 
> > given the error before without any problem, but eventually 
> stops at a 
> > later time (varying between tens to hundreds of ps) with a similar 
> > error, but on a different atom.
> 
> what pressure coupling constants do you use? try to use at least 1 ps.
> > I hope you can help me with this.
> > Thanks
> --
> David.
> ______________________________________________________________
> __________
> 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://xray.bmc.uu.se/~spoel
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