[gmx-users] trjcat error of different spacing

[Justin A. Lemkul]

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

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