[gmx-users] trjconv problem

Bjoern Windshuegel bjorn.windshugel at uku.fi
Sat Aug 5 09:09:40 CEST 2006


thanks for the tips. First I used the information of the exact time I got from 
g_cluster which did not work (t=5590.093). So I used trjconv to convert the 
whole trajectory in a pdb-file from which I got the exact time (t=5590.00049) 
of the frame to be extracted that was different compared to that in 
g_cluster. By using that as input for trjconv I finally could extract the 
The -dump option did not work without specifying the exact frame time.

Best regards,


> 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


>similar happened to me, when i used the -b and -e flags of trjconv. to me it 
>seemed that if you do not hit exactly the time frame as written in the trr 
>file, trjconv will not output anything. when i used the -dump flag it worked, 
>because then frames near the specified time are dumped. hope that helps.


Bjoern Windshuegel

Department of Pharmaceutical Chemistry
University of Kuopio
Harjulantie 1
70211 Kuopio, FINLAND

Phone: (+358) 17 162463
Fax:   (+358) 17 162456

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