[gmx-users] Fatal error: Frame contains more atoms than expected

[David]

On Wed, 2004-05-19 at 16:18, SANTINI sebastien wrote:
> > >
> > > It seems the problem came from the peptide (a dimer) that went out of the
> > > box.
> > >
> > > using a larger box with the comm_mode = Linear the crash does not happen
> > > anymore (but i'm still waiting for longer simulations).
> >
> > do you mean you had the comm-mode = angular when the crash happened, but
> > with comm-mode = linear it works?
> >
> 
> (maybe it's important : I use GROMACS 3.1.4)
> 
> I used comm-mode = angular in my mdp file but I think this option was not 
> taken into account because I have a warning : line unknown in the mdp file.
> When I look to the trajectory, the dimer move out of the box.
> Using comm-mode = linear the center of mass is replaced in the center of the 
> box.
> my protein AND my box are asymetric so I have just increased the size of the 
> box, then if the protein rotate it can not go out of the box.
> 
> Am I wrong ?
It shouldn't matter, and comm_mode = angular should work as well, that's
why I'd like to hear when it does not work in a reproducible manner.

There are many documented and undocumented reasons to upgrade though..

-- 
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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