[gmx-users] again gmxcheck

[David van der Spoel]

Grazia Daminelli wrote:
> hello everybody!
> 
> I would like to check if there is any problem in my topology file. By using
> gmxcheck -f traj.trr -s1 topol.tpr
> I get an incredible long list of the type:
> 
> Distance between atoms 1 and 2 is 0.101, should be 0.010
> Distance between atoms 1 and 3 is 0.100, should be 0.010
> Distance between atoms 1 and 4 is 0.102, should be 0.010
> Distance between atoms 1 and 5 is 0.150, should be 0.022
> Distance between atoms 5 and 6 is 0.153, should be 0.023
> Distance between atoms 5 and 9 is 0.153, should be 0.023
> ....
> 
> Atoms from 1 to 10 belong to the serine residue, so that atom 1 is N, 
> atoms 2,3,4 are H, atom 5 is CA.
> I have problems in understanding the above output:
> 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, 
gmxcheck
provides a quick check for such problems.

So are you sure the tpr file and the trajectory match?

> 
> thanks for any comment/explanation
> 
> Grazia
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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