[gmx-users] Analysis programs and PBC.

[Maxim Fedorov]

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.

My best wishes,

Maxim



>