[gmx-users] Analysis programs and PBC.

Daniela S. Mueller D.S.Mueller at rug.nl
Wed Mar 1 00:49:40 CET 2006

Dear Maxim,

On Mon, 2006-02-27 at 18:14 +0000, Maxim Fedorov wrote:
> Dear Daniela, dear all.
> Sorry, my previous reply was corrupted 
> by our server - as a result it lost any sense.
> You wrote:
> > 
> > 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,
> What do you exactly mean when you are saying 'subunits' - some separate
> molecules or different functional parts of the SAME molecule like
> residials in polypeptide/protein chain or sugars in a polysaccharide, etc?
> Your answer is of crucial importance for me - now I have only one
> molecule (polypeptide) but it contains many residials.

As Anton already said, a subunit of a protein is a distinct molecule.
The protein I mentioned consisted of two (separate) chains which can
jump over the box boundaries independently, so that the complex
appears(!!!) to separate (while of course the chains are still
interacting across the periodic boundary). 
If you have one chain, you don't have to worry about jumps. 

Best regards, 

> My best wishes,
> Maxim


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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