VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 23 2006 - 10:34:03 CDT

Hi,
  Depending on which "weight" you use with 'measure center', you might be
getting zero-values for weights if your structure has atomic masses of
zero, or perhaps ridiculously large weight values from bad units.
Can you show me the actual commands you used when calling 'measure center'?

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 23, 2006 at 11:22:49AM -0400, Ana Celia Araujo Vila Verde wrote:
> Hi all,
>
> I am experiencing a problem with the "measure" command. I am using it to determine the minimum and maximum values of the coordinates in my simulation box and also its geometric center. In my case, I am simulating a droplet of water on gold.
>
> If I calculate the minmax and the center for the water, I get perfectly reasonable values.
> If I calculate the minmax and the center for the gold, I also get reasonable values
> However, when I calculate the center for the entire system, I get a Z coordinate which is entirely unreasonable: 8.27, instead of the expected 25.6 !!!! Can someone help me understand what is going on here?
>
> Please see below the output that I got:
>
> water minmax
> {82.4457626343 82.3411026001 12.1560001373}
> {119.096755981 119.577102661 49.2019996643}
> water center
> 100.929145813 100.934669495 30.4673595428
>
> gold minmax
> {0.0 0.0 2.03900003433}
> {201.860992432 201.860992432 8.15600013733}
> gold center 100.930107117 100.930007935 5.09764385223
>
> all minmax
> {0.0 0.0 2.03900003433}
> {201.860992432 201.860992432 49.2019996643}
> all center
> 100.928276062 100.93032074 8.27163791656
>
>
>
> Thanks,
>
> Ana
>
>
>
>
> _________________________________
> Ana Célia Araújo Vila Verde
> Penn State University
> Department of Chemical Engineering
> Fenske Laboratory
> University Park, PA 16802
> USA
>
> <http://www.gfct.fisica.uminho.pt/Members/acvv>
> Phone: +(1) (814) 863-2879
> Fax: +(1) (814) 865-7846
> avilaverde_at_engr.psu.edu
> http://www.che.psu.edu/Faculty/JMaranas/group/avv.html
> http://www.gfct.fisica.uminho.pt/Members/acvv
> _________________________________
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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