[gmx-users] Mdrun box nan error
Nathalie R. Basdevant
nrb2001 at med.cornell.edu
Fri May 7 19:05:01 CEST 2004
Thanks fir your reply. I am using 1ps for pressure coupling should I use a
larger constant .e.g 5-10ps?
> -----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
> > 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
> > -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 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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