VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 05 2011 - 13:59:28 CDT

Jesper, Axel,
  Another issue that people often forget about is that the periodic cell
information is not always fully encoded in the trajectory files saved
by the simulation tools. I would not describe the addition broad support
for periodic boundary conditions as requiring a rewrite personally.
It is easy to add support for periodicity incrementally.
The biggest problem in my view is handling all of the different periodic
cell description conventions in the plugin APIs and being able to cleanly
convert between these conventions without errors when users load different
files. Many trajectory files don't even fully specify all of the periodic
cell information that one needs to do these things correctly. Anyway, it
remains an ongoing project to address this, among many other things we're
currently working on. Right now the main thing I am working on is getting
out-of-core visualization and analysis working in VMD, and that is
currently taking up all of my free time.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Jul 03, 2011 at 06:30:43PM +0200, Jesper Sørensen wrote:
> 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.
> 

-- 
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