From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Sep 04 2012 - 01:53:15 CDT
I think it would make sense to add such a warning at a system building
stage, maybe for psfgen. Such a "simple" structure check is also implemented
in the amber tools. For example, when doing saveamberparm in xleap, which is
the same as psfgen for charmm, messages like "Close contact between x and y"
or "There is an bond of 7A between x and y" or "The total charge of the
system is not zero". At this stage of using VMD as a system building tool
(and not as visualizer) it would be a nice thing IMHO.
Nevertheless, if someone builds a system, set a box dimension, solvate it,
then use different cell size in the simulation and wonders about
superimposed atoms, even such a feature can't help. -_-
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Axel Kohlmeyer
> Gesendet: Montag, 3. September 2012 22:28
> An: Rajan Vatassery
> Cc: amin_at_imtech.res.in; Norman Geist; namd-l_at_ks.uiuc.edu
> Betreff: Re: AW: AW: AW: namd-l: Error in membrane protein simulation
> Well then here is your chance to win the eternal gratitude of all VMD
> or NAMD users that share your sentiment.
> ------Original Message------
> From: Rajan Vatassery
> To: Axel Kohlmeyer
> Cc: amin_at_imtech.res.in
> Cc: Norman Geist
> Cc: namd-l_at_ks.uiuc.edu
> ReplyTo: Rajan Vatassery
> Subject: Re: AW: AW: AW: namd-l: Error in membrane protein simulation
> Sent: Sep 3, 2012 10:15 PM
> looks like we agree that it would be easy to do.
> On Mon, 2012-09-03 at 22:13 +0200, Axel Kohlmeyer wrote:
> > On Mon, Sep 3, 2012 at 10:03 PM, Rajan Vatassery <rajan_at_umn.edu>
> > > On a related note, I think VMD could add an error message
> in cases
> > VMD is a visualizer there doesn't care much what kind of data you
> feed it.
> > > where atoms are superimposed. While it wouldn't be widely useful,
> > > would be easy enough to implement that it would be worthwhile
> > > expenditure of time.
> > you can easily write such a check with a few lines of VMD script
> > (loop over all atoms, create a selection with a reasonably short
> > around the current atom index, count the atoms in the selection, if
> > more than 1 throw a warning, delete the selection).
> > cheers,
> > axel.
> > > rajan
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
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