[gmx-users] g_gyrate

[David]

On Fri, 2005-04-01 at 09:49 -0800, Nancy Deng wrote:
> Hi David,
> 
> thanks for the reply.  the 2ns.trr file is nearly 900Mb. And my simulation
> was done at Linux cluster on multiple nodes.
> 
> The complain is saying "trn" file. I also try "trjconv" to convert the
> ".trr" to ".xtc", the program stop at the same place with the same fatal
> error "Can not determineprecision of trn file, quit!".
Run gmxcheck on the file, it seems that it has been corrupted in some
way.
If it's corrupt then there is not much you can do about it. Restart the
simulation from the last correct frame that has coordinates and
trajectories.

> 
> Interesting thing is that another similiar system containing the same
> protein but with ligand in its binding cavity stopped at 1290ps with the
> same error.
> 
> However, if I use "ngmx" to view the trajectory, it looks fine.
> 
> Thank you so much for your any suggestions.
> 
> nancy
> 
> ----- Original Message ----- 
> From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Thursday, March 31, 2005 10:56 PM
> Subject: Re: [gmx-users] g_gyrate
> 
> 
> > On Thu, 2005-03-31 at 15:24 -0800, Nancy Deng wrote:
> > > Dear All,
> > >
> > > I have done 2ns MD with gmx_FF and was trying to calculate the radius
> > > of gyration of the entire protein by: g_gyrate -s 2ns.tpr -f 2ns.trr -
> > > o 2ns.xvg
> > >
> > > The program stopped at 560ps with the "fatal error: Can not determine
> > > precision of trn file, quit!"
> > >
> > > Does any one please have any idear what really happend here??? what's
> > > the trn file?
> > the trr file I assume. Is the file larger than 2 Gb ? Then look for 2 Gb
> > patches in the mailing list archives.
> > >
> > > Thanks,
> > >
> > > nancy
> > >
> > >
> > >         ----- Original Message ----- 
> > >         From: narender maan
> > >         To: gmx-users at gromacs.org
> > >         Sent: Thursday, March 24, 2005 10:54 AM
> > >         Subject: [gmx-users] g_anaeig
> > >
> > >
> > >         Dear gmx-users
> > >         I am doing ED of my simulation and while using g_anaeig the
> > >         file (eigrmsf.xvg) i am getting for rmsf (by using -rmsf
> > >         option) is for all the atoms in the protein. So i was
> > >         wondering if there's anyway to calculate averages for each
> > >         residue in eigrmsf.xvg instead of atoms (like the way it is in
> > >         g_rmsf by using the option of -res)
> > >         thank you
> > >         NSM
> > >
> > >
> > >         ______________________________________________________________
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> > -- 
> > 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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> 
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-- 
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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