Re: AW: AW: AW: Error in membrane protein simulation

From: Axel Kohlmeyer (
Date: Mon Sep 03 2012 - 15:28:20 CDT

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: Norman Geist
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 <> wrote:
> > 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, it
> > 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 code.
> (loop over all atoms, create a selection with a reasonably short cutoff
> around the current atom index, count the atoms in the selection, if it
> more than 1 throw a warning, delete the selection).
> cheers,
> axel.
> > rajan

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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