From: Axel Kohlmeyer (
Date: Thu Mar 27 2008 - 06:06:17 CDT

> Matt Watkins wrote:
> > Yes, thanks that works beautifully. So all you materials chemistry type
> > people use 'pbc wrap -nocompound ...'
> In fact, I'm pondering whether to change the default to be "-nocompound"
> instead of "-compound residue" since quite some time, as many newbiew
> questions arise from that.
> The reason for the default is, that the "original" wrapping code used
> it, and I didn't dare to simply change it.
> So, what do you, i.e. the other users and developers of pbctools, think
> of changing the default?

whatever choice you make, there will always be people that find this unexpected.

just think about all the "bio-people" that will have their water
molecules "chopped"
when you make -nocompound the default (and complain about it).

it is the privilege of the maintainer of a package to choose.

BTW, it may be convenient to include an -updatebonds (default off) flag
that will call 'mol bondsrecalc <mol>' after the (final) wrap.


> Olaf
> Version: GnuPG v1.4.6 (GNU/Linux)
> Comment: Using GnuPG with Mozilla -
> iD8DBQFH60z4tQ3riQ3oo/oRAreCAJ9QJxOV08RdGCxGsr0R8UP5JalEKgCgk0mr
> ELrBrzvtDDyAWwpsnJe46l0=
> =QMiu

Axel Kohlmeyer
 Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.