[gmx-users] Fatal error: Frame contains more atoms than expected
spoel at xray.bmc.uu.se
Wed May 19 23:37:27 CEST 2004
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
> 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 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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