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, Daniela > My best wishes, > > Maxim > > > -- Daniela S. Mueller biologist (Diplom, German degree) ______________________________________________________________________ - Molecular Dynamics Group, UQ - Address: School of Molecular and Microbial Sciences (SMMS) Chemistry Building (#68) University of Queensland Qld 4072, Brisbane Australia Phone: +61-7-33653732 Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm ********************************************************************** - MD group, RuG - Address: Molecular Dynamics Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Website: http://www.rug.nl/gbb/md ______________________________________________________________________ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
