[gmx-users] -ndec 30

[David]

On Tue, 2003-11-11 at 18:51, Nguyen Hoang Phuong wrote:
> On 11 Nov 2003, David van der Spoel wrote:
> 
> > On Tue, 2003-11-11 at 12:52, Nguyen Hoang Phuong wrote:
> > > Dear All,
> > >
> > > I did run the simulation for 100ps and I would like to continue for
> > > another 100ps. In the second run, the input file of coordinates and
> > > velocities are taken from the first trajectory with the option -t when
> > > running grompp.
> > >
> > > Alternatively, I use trjconv to convert the last snaphshot of the first
> > > trr file to the gro file with the option -ndec 30 (30 number of decimal
> > > place) to make sure that the precision of this file is as high as that of
> > > trr file. If I start the second run from this gro file then the
> > > simulation is crashed. If -ndec 6 or -ndec 15 etc. then OK. Thanks in
> > > advance for any explainations.
> >
> > have you looked at the gro file? Is it OK? Are the first decimals the
> > same as in the -ndec 6 case?
> >
> 
> yes, they are the same. I know why the simulations are crashed.
> 
> Using (trjconv -ndec 30 -o xx.gro) I got a file name xx.gro and then do
> (trjconv -f xx.gro -ndec 30 -o xx.trr) I got the file xx.trr. The
> simulations starting with xx.trr are crashed because the coordinates and
> velocities in this file are not correct (containning some strange
> numbers).
> 
> Does anyone know the reason?

yes, the gro file that you generate with -ndec 30 is not a valid gro
file anynmore. It is read with fixed positions for the coordinates. You
might want to try g96 files.

> 
> Phuong
> 
> > > _______________________________________________
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> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assist. 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, Assist. 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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