[gmx-users] discrepancy trjconv and gmxdump

Gavin Melaugh gmelaugh01 at qub.ac.uk
Wed Nov 2 13:56:09 CET 2011

Actually Mark, I may have made a very trivial error. Forget about it for



Gavin Melaugh wrote:
> Hi Mark
> My Apologies. Here is more info.
> gmxdump -f traj.trr >history
> >From history I take the coordinates at 250 ps and convert to gro file
> say test.gro
> trjconv -f traj.trr -dump 250 -o frame5.gro
> I then compare frame5.gro with test.gro
> Please find attached an excerpts of both files (in one file) and pay
> attention to the sign difference of the x coordinate at atom s 38 50 51 59
> Cheers
> Gavin
> Mark Abraham wrote:
>> On 2/11/2011 10:23 PM, Gavin Melaugh wrote:
>>> Hi all
>>> I have generated a gro file from a traj.trr file using trjconv. When I
>>> use gmxdump on the same traj.trr file to output a generic format history
>>> file it seems that there is a discrepancy in the coordinates of some
>>> atoms in a particular frame. Essentially I output frame 5 using trjconv,
>>> then I take the corresponding frame from the history file and covert it
>>> to gro format. I then run vimdiff on the two files. There are sign
>>> differences with the coordiante components. The atoms in question are at
>>> the edge of the periodic box. I was just wondering why there is a
>>> discrepancy in the two utilities?
>> Without actual command lines that produced output and actual examples
>> of what you think is anomalous we can't say.
>> Mark

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