[gmx-users] Analysis programs and PBC.

Maxim Fedorov maxim.fedorov at ucd.ie
Mon Feb 27 17:56:52 CET 2006

Dear Daniela,

> If the molecule you want to analyse is a single molecule, the 
> jumping of
> box boundaries does not matter and the analysis tools take that into
> account. But if your molecule is a complex of two or more separate
> subunits, you might want to remove jumps over the boundaries to
> reassemble the complex again, e.g. to measure the minimum distance to
> the periodic images (and not to the subunit, which should be very
> nearby). 
> What I actually found with trjconv -pbc nojump was, that two 
> conditionsapply if you want to remove jumps: 1) the trajectory has 
> to start at the
> initial frame and be continuous; 2) the tpr-file should correspond to
> the initial conformation. If these conditions weren't fulfilled, 
> one of
> the subunits was rotated and the complex was reassembled 
> incorrectly -
> although the box was rectangular. 
> This incorrect rotation seems to be a weird bug, probably the
> referencing to the tpr-structure is a special case-treatment and not
> robust to various setups...? 

Thank you very much for this information.
Could you specify in more details what do you mean when you
Could it be residials of a polypeptide/protein chain or
you mean something else?

All the best,


> Success and best regards, 
> Daniela

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