VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Jul 03 2011 - 11:21:39 CDT

2011/7/3 Jesper Sørensen <lists_at_jsx.dk>:
> Hi all,
>
>
>
> I have read a few old posts about the command “measure contact” and that it
> does not work when the two selections are split by the periodic boundary. Is
> this still the case?

yes.

> I cannot find a note on it in the current VMD user’s guide.

given VMDs development history you should always assume
that there is no PBC support unless explicitly notes.

making commands in VMD "silently" PBC aware has a number
of unexpected implications considering how many people have
written elaborate scripts or packages that expect a certain
behavior. on top of that is the fact, that a lot of PBC related
options (e.g. periodic display of representations) are more like
an afterthought rather than a from ground up designed feature.

it is a pity, since it can be pretty frustrating as a user, but
outside of starting a VMD 2.0 development effort that would
include periodic cell data management from ground up, there
are only limited options as to what can be done. the only
saving grace at the moment is that you can write your
custom scripts and plugins to try alleviate the shortcomings.
imagine you would not have even that..

cheers,
    axel.

>
>
> Best,
>
> Jesper 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.