[gmx-users] RE: again gmxcheck

Grazia Daminelli Grazia.Daminelli-Widany at TU-Berlin.DE
Tue Feb 21 09:32:03 CET 2006

hello David

>>> is there a unit problem when comparing trajectory and tpr files ?
>>> can it be that N is called atom 1 in the trajectory file and atom 0 in 
>>> the topol.tpr file?
>>> if gmxcheck is working correctly, then my  topol.tpr is completely 
>>> wrong, how  can I find out  the mistake?
> From gmxcheck -h :
>If both a trajectory and a tpr file are given (with -s1) the program will
>check whether the bond lengths defined in the tpr file are indeed correct in
>the trajectory. If not you may have non-matching files due to e.g.
>deshuffling or due to problems with virtual sites. With these flags, 
>provides a quick check for such problems.
>So are you sure the tpr file and the trajectory match?
thanks for your answer.
well, I am not working in parallel and I don't have virtual sites, so I 
was already excluding non-matching problems related to these cases. What 
else could it be and how do I check if files are matching or not?
I tried with gmxdump -s topol.tpr and indeed the first atom in topol.tpr 
is a N and has number 0, but I thought this is always the case.
btw I have just tried gmxcheck -f traj.trr -s1 topol.tpr on the tutorial 
files... also there I get this long list ... what am I doing wrong?

thanks again


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