VMD-L Mailing List

From: Jesper Sørensen (lists_at_jsx.dk)
Date: Sun Jul 03 2011 - 11:30:43 CDT

Hi Axel,

Thanks for the quick reply.
I have overcome this problem in the past doing other analyses, by simply
creating a box containing the mirror images in each direction. The problem
that I am faced with now, might not allow such a "simple" solution. I'll
give it some more thought...

A VMD 2.0 effort including this would be great... hint hint VMD group ;-) I
am of course aware of the huge development work/resources that would
require.

Thanks again,
Jesper

 
-----Original Message-----
From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
Sent: 3. juli 2011 18:22
To: Jesper Sørensen
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: contacts and pbc

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.