VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Thu Dec 08 2005 - 14:21:17 CST

John,

Thanks for your quick reply. I see the problem from the point of view of NAMD
users, who mostly use VMD for viewing and analyzing NAMD-generated
trajectories.
Since NAMD only wraps whole molecules across the periodic cell boundaries, no
covalent bonds cross these boundaries - unless the coordinates are tampered
with afterwards. I suppose most programs running classical MD simulations
behave in a similar manner.

Therefore, I would suggest that your first three items (i.e., those dealing
with non covalently bonded atoms) are more relevant to most of us than the
other three. But it would certainly be interesting to read the opinion of
other VMD users on this list.

Jerome

Le Jeudi 08 Décembre 2005 20:40, John Stone a écrit :
> Jerome,
> We should probably create new PBC-aware versions of the
> existing VMD functions that do:
> - 'within' and 'exwithin' atom selections
> - 'measure contacts'
> - 'measure hbonds'
> - automatic bond search (allow bonds across PBC cell boundaries)
> - draw bond components of the Bonds, CPK, and Licorice representations
> - draw dynamic bonds representation
>
> Adding PBC-awareness to the drawing code is the most risky in terms
> of hurting performance, but this may be something that could be dealt with
> by adding a checkbox so that VMD only spends effort checking for this when
> the user actually needs it.
>
> Before embarking on implementing all of this, it would be nice to know
> which of these users would find most beneficial. We could work on the
> most-wanted features first...
>
> John Stone
> vmd_at_ks.uiuc.edu 

-- 
Jérôme Hénin
Equipe de Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS
Tel : (33) 3 83 68 43 91        Fax : (33) 3 83 68 43 71
http://www.edam.uhp-nancy.fr/