[gmx-users] problem in making a trajectory

[francesca vitalini]

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.

Thanks in advance for all the help.

Francesca

2012/6/16 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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
>
> --
> ==============================**==========
>
> 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<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
francesca.vitalini at fu-berlin.de

+49 3083875776
+49 3083875412
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