[gmx-users] trjconv problem

[Jochen Hub]

Bjoern Windshuegel wrote:

>Hi everybody,
>
>I am trying to extract some frames from my md simulation using trjconv. For 
>some frames this works fine but for others of the same simulation I get the 
>following error message (for frame after 5590 picoseconds):
>
>Skipping frame    500 time 5250.000
>
>Setting output precision to 0.001 (nm)
>
>WARNING no output, trajectory ended at 5590
>
>
>The trajectory has a length of 10 ns. I could successfully extract frames for 
>4310 and 8950 but not 3110, 5590 and 7020 picoseconds. Any idea what could be 
>the problem?
>
>
>Best regards,
>
>Björn
>
>
>
>
>  
>
It might be a rouding problem, so if you want to extract the single 
frame at time 5590, you might want to try

trjconv -b 5589.9 -e 5590.1 -o frame.pdb ...

If it still doesn't work:
In gromacs 3.3 there was a bug that caused trjconv not to find frames.  
As far as I know the bug was fixed in Version 3.3.1.

cheers, jochen

-- 
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************