[gmx-users] Re: gmx-users digest, Vol 1 #568 - 6 msgs

Outi Maija Salo osalo at messi.uku.fi
Mon Jan 13 08:35:01 CET 2003

> On Fri, 2003-01-10 at 11:36, Outi Maija Salo wrote:
> > Hi!
> >
> > What could be the problem with my mdrun if it collapses after the
> > beginning and informs like this:
> >
> > Warning: Only triclinic boxes with the first vector parallel to the x-axis
> > and t
> > he second vector in the xy-plane are supported.
> >          Box (3x3):
> >             Box[    0]={         nan,          nan,          nan}
> >             Box[    1]={         nan,          nan,          nan}
> >             Box[    2]={         nan,          nan,          nan}
> >          Can not fix pbc.
> You have very large forces for some reason. Is this in the beginning of
> the run? THen you need to do more minimization. Do also check whether
> you have periodic bondary problems.

Yes, this is the very beginning of the run. Could the large forces be due
to the TIP4P water box and opls force field?
This same calculation works on SGI but not on Linux machine...
so the problem should not be in pbc; or if it is, how can I know what it


Outi Salo
University of Kuopio

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