VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 25 2004 - 13:28:37 CST

Markus,
  There could be several reasons for the differences you mention.
One could implement distance based atom selections a number of ways,
but they aren't actually the same thing. For example, do you only
return the atoms for which the atom centers fall within the distance
cutoff, or do you also return atoms for which any part of the atom
(i.e. based on its radius) falls within the cutoff distance, or do you
only return atoms that are entirely within the cutoff distance?

Since I don't know anything about how Charmm implements its ".around"
command, I can't really say what the differences are, but I suspect that
VMD and Charmm are doing a slightly different type of cutoff calculation.

Keep in mind that if you make a selection such as "within 5 of (xxxx)"
if VMD and Charmm implement 'xxxx' differently, then you'll also get
differing results. Since you didn't mention what selections you actually
tried, I don't have any other suggestions for you to try.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 25, 2004 at 03:23:37PM +0100, Wagener, M. (Markus) wrote:
> Hi,
>
> while comparing distance based atomselections made with
> charmm (using ".around.") and with vmd (using "within")
> I noticed some small differences. Are there any issues known?
>
> BTW, I am using vmd V1.8.1 on IRIX and CHARMm V29.1
>
> Cheers,
> Markus
>
>
> --
> -----------------------------------------------------------
> Dr. Markus Wagener
> NV Organon
> MDI-CMC RK2330 phone: +31-412-661380
> P.O. Box 20 FAX: +31-412-662539
> 5340 BH Oss Email: markus.wagener_at_organon.com
> The Netherlands
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