[gmx-users] pull code for speptide

Frauke Meyer fmeyer at ix.urz.uni-heidelberg.de
Tue Aug 12 04:40:01 CEST 2003

On Mon, 11 Aug 2003 ysun at mie.utoronto.ca wrote:

> Thanks to Marc,
> I am not sure if Gromacs could stretch on a group of molecules?
Well, I *am* using the pull code to pull the termini of a protein away
from each other - you can use it for this purpose I would say.

> I WOULD appreciate if you could advise me more detail and suggest how to modify
> my pull code.
> >  mdrun -s prpull3.tpr -o prpull3 -c prpull3.gro -e prpull3.edr -g
> > prpull3.log
> >  -
> >  pi pull.ppa -pn index.ndx
> >
> >  The error came out:  "floating exception"
> >
On what machine are you running it (which os)? Does the job run on another
without problems? Does it occur right before the first step, and is it due
to the pull code (just skip -pn and -pi and see what happens)?
I had that problem on a Dec Alpha cluster with OSF as operating system.
As for step=0 the force equals zero, one of the functions (increment of a
vector) caused the error, but this seems to very much depend on the
floating number/error handling.


Frauke Meyer
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park
Shanghai 201203
Tel: +86 21 50806600*1201, Fax: +86 21 50806600*1205
http://www.dddc.ac.cn, e-mail:frauke.meyer at mpi-bpc.mpg.de

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