[gmx-users] discrepancy trjconv and gmxdump

Gavin Melaugh gmelaugh01 at qub.ac.uk
Wed Nov 2 13:38:55 CET 2011

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


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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