Hello Francesco,

I must say you are taking us into deeper waters than many of us have ever ventured (you sound like a oceanologist). Certainly not many people seem to have the experience with pivot install, or even running scientific programs from a pivot_install. So my advice is based on my limited knowledge of this area.

It is true that hd install changes knoppix into debian...........
Well, not exactly. A special form of Debian that is prone to problems, but that's a long story.

BASIC 1st QUESTION about pivot_root install on external hd: the external hd is made ROOT, so that any file there is root root, unless one goes to chown. Correspondingly, the kde konsole has prompt # for root only.
Yes I think this is correct. But you can try to su to a different user instead of root.

Is that the correct way of running debian-knoppix under pivot_install?
There is no right or wrong way -- you are in uncharted waters here. You have a very special situation, so do whatever works.

Does this mean that in order to have something read (such as setting of environmental variables) by .bashrc at boot I have to write my needs to
/etc/profile
? Obviously because external hd is made root, scripts (such as setting environmental variables) in

/home/francesco/.bashrc

are not felt.
Yes, I think that is correct.

I am only stopped at the moment because my molecular modeling package does not accept libXm.so.3 from the STABLE Debian distribution of package libmotif3 (problems with Open Motif affect Debian from long time, which creates problems to science, where graphics is based on that).
Is this molecular package open source and downloadable as a Debian package? If I can get hold of it, I'll see if I can discover something useful as a fix.

Regards.