[gmx-users] trjcat error of different spacing

[Anirban Ghosh]

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?

Thanks,

Anirban

On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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