[gmx-users] Analysis programs and PBC.

Daniela S. Mueller D.S.Mueller at rug.nl
Tue Feb 28 00:16:31 CET 2006

Hi Maxim, 

On Mon, 2006-02-27 at 16:56 +0000, Maxim Fedorov wrote:
> 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?

The protein consists of two chains. During the simulation, one of the
chains jumped across the box boundary while the other one stayed on the
original side of the box. After using trjconv -pbc nojump on a
trajectory fragment starting at a time after the jump, the chain is
transformed into the box but with a rotation. 
It's pretty tricky because you have to be able to recognise this as the
wrong assembly, otherwise you would just continue working with a wrong

I will see if I can submit a bugzilla. 


> All the best,
> Maxim.
> > 
> > Success and best regards, 
> > Daniela
> > 


Daniela S. Mueller

biologist (Diplom, German degree)

- Molecular Dynamics Group, UQ -

School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane

Phone: +61-7-33653732

Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm


- MD group, RuG -

Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Website: http://www.rug.nl/gbb/md

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