[gmx-users] problem in making a trajectory

[Justin A. Lemkul]

On 6/16/12 7:54 AM, francesca vitalini wrote:
> yes and I do.
> By the way the version of GROMACS I'm using is the 3.3.1, I forgot to specify
> that before.
>

OK, I see the same with version 4.5.5, but a trajectory is produced from my set 
of .gro files and it is correct.

Continue writing frames from md_0_25.gro t=0 ps, frame=0
Last frame          0 time    0.000
WARNING: Frames around t=0.000000 ps have a different spacing than the rest,
might be a gap or overlap that couldn't be corrected automatically.
Reading frames from gro file 'Raft G96 system in water', 60523 atoms.
Reading frame       0 time    0.000
WARNING: Couldn't find a time in the frame.

lasttime 0

Continue writing frames from md_25_50.gro t=25 ps, frame=1
Last frame          0 time    0.000
WARNING: Frames around t=25.000000 ps have a different spacing than the rest,
might be a gap or overlap that couldn't be corrected automatically.
Reading frames from gro file 'Raft G96 system in water', 60523 atoms.
Reading frame       0 time    0.000
WARNING: Couldn't find a time in the frame.

lasttime 25

The key is to note that it is setting the times specified.  Do you get an .xtc 
file?  What does gmxcheck tell you about it?

-Justin

>
> 2012/6/16 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
>
>
>     On 6/16/12 7:41 AM, francesca vitalini wrote:
>
>         Dear Justin,
>
>         this is my trjcat command
>
>           /home/cocktail/vitalini/__gromacs_special/bin/trjcat -f
>         /home/cocktail2/vitalini/__reverse_transformation_vacuum/__300-65-100/300-65-100___annealing.gro
>         /home/cocktail2/vitalini/__reverse_transformation_vacuum/__300-65-100/300-65-100___annealing2.gro
>         /home/cocktail2/vitalini/__reverse_transformation_vacuum/__300-65-100/300-65-100_min.gro
>         /home/cocktail2/vitalini/__reverse_transformation_vacuum/__300-65-100/300-65-100_min1.gro
>         -o
>         /home/cocktail2/vitalini/__reverse_transformation_vacuum/__300-65-100/300-65-100_traj___tot.xtc
>         -settime -cat
>
>         I'm using the settime command to have each structure at a different time
>         step.
>         If I was using it wrongly please correct me.
>
>
>     You should be prompted to then set a time value for each frame, is that not
>     the case?
>
>
>     -Justin
>
>     --
>     ==============================__==========
>
>     Justin A. Lemkul, Ph.D.
>     Research Scientist
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
>     ==============================__==========
>
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> --
> Francesca Vitalini
>
> PhD student at Computational Molecular Biology Group,
> Department of Mathematics and Informatics, FU-Berlin
> Arnimallee 6 14195 Berlin
>
> vitalini at zedat.fu-berlin.de <mailto:vitalini at zedat.fu-berlin.de>
> francesca.vitalini at fu-berlin.de <mailto:francesca.vitalini at fu-berlin.de>
>
> +49 3083875776
> +49 3083875412
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================