[gmx-users] problem in making a trajectory

Justin A. Lemkul jalemkul at vt.edu
Sat Jun 16 13:10:45 CEST 2012

On 6/16/12 6:48 AM, francesca vitalini wrote:
> Dear Gromacs Users,
> While making a trajectory connecting different gro files I got the following
> output which I don't understand.
> Continue writing frames from
> /home/cocktail2/vitalini/reverse_transformation_vacuum/300-166-160/300-166-160_annealing.gro
> t=1 ps, frame=0
> Last frame          0 time    0.000
> WARNING: Frames around t=1.000000 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 'Protein', 15230 atoms.
> Reading frame       0 time    0.000
> WARNING: Couldn't find a time in the frame.
> Can anyone explain to me the implication of this warning message?

Trajectories need time information, .gro files don't have any.  In the absence 
of your trjcat command, I can only assume you're not using -settime to specify 
what time point to which each frame corresponds.  If that's not the case, please 
provide the command you are using.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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