[gmx-users] trjcat error of different spacing

[Justin A. Lemkul]

Anirban Ghosh wrote:
> Hello Justin,
> 
> Thanks for the reply.
> gmxcheck on the first trajectory shows:
> 
> -------------------------------------------------------------------------------------------------
> Checking file protein_3000NS_2.trr
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time 2957280.000  
> # Atoms  57296
> Reading frame    1400 time 2999280.000  
> 
> Item        #frames Timestep (ps)
> Step          1425    30
> Time          1425    30
> Lambda        1425    30
> Coords        1425    30
> Velocities    1425    30
> Forces           0
> Box           1425    30
> ---------------------------------------------------------------------------------------------------
> 
> And on the second trajectory shows:
> 
> ---------------------------------------------------------------------------------------------------
> Checking file B2AR_self_assembly_3500NS.trr
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time 3000000.000  
> # Atoms  57296
> Reading frame   16000 time 3480000.000  
> 
> Item        #frames Timestep (ps)
> Step         16667    30
> Time         16667    30
> Lambda       16667    30
> Coords       16667    30
> Velocities   16667    30
> Forces           0
> Box          16667    30
> ---------------------------------------------------------------------------------------------------
> 
> So gmxcheck does not show any warning/error.
> Then why I am getting the warning from trjcat. And how to remove it?
> 

I don't know yet.  A few more questions:

1. What version of Gromacs are you using?

2. How many total trajectories are you concatenating?  You said there was a 
problem from 10 -> 3000000 ns, but I don't see any times shown here below 
2957280.  The real problem could be early on in the trajectory.

-Justin

> Thanks,
> 
> Anirban
> 
> On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Anirban Ghosh wrote:
> 
> 
>         Hi ALL,
> 
>         I am trying to use trjcat -f input files -o output_file to join
>         to very larger trajectories. However I am getting the following
>         error:
> 
>         -------------------------------------------------------------------------------------------------------------------------------------------
>         Continue writing frames from protein_3000NS_2.trr t=2.95728e+06
>         ps, frame=98576      ->  frame 100000 time 3000000.000 ps     ->
>          frame  99980 time 2999400.000 ps    WARNING: Frames around
>         t=3000000.000000 ps have a different spacing than the rest,
>         might be a gap or overlap that couldn't be corrected automatically.
>         Reading frame       0 time 3999990.000  lasttime 3e+06
> 
>         Continue writing frames from protein_4000NS.trr t=3.99999e+06
>         ps, frame=100001  
>         -------------------------------------------------------------------------------------------------------------------------------------------
> 
>         And if I use this resultant output trajectory for further
>         analysis like g_sas, then a portion between around 10 ns and
>         3000000 ns is simply joined by a straight line.
>         How to remove this inconsistency from the two trajectories?
>         Any suggestion is welcome.
> 
> 
>     What does gmxcheck tell you about each of the individual
>     trajectories (prior to running trjcat)?
> 
>     -Justin
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

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

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

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