From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Fri Jun 23 2006 - 11:02:14 CDT

Hi John,
 
Thank you for being willing to look into this. I just used the standard commands, with no weights. Here they are:
##############################################################################
# recalculating minmax and center for the new system, after the water atoms have been moved.
set wat [atomselect top water ]
puts $out2 "final water minmax [measure minmax $wat]"
puts $out2 "final water center [measure center $wat]"
 
set gold [atomselect top "resname Au"]
puts $out2 "gold minmax [measure minmax $gold]"
puts $out2 "gold center [measure center $gold]"
 
set all [atomselect top all]
puts $out2 "all minmax [measure minmax $all]"
puts $out2 "all center [measure center $all]"
set chrg [eval "vecadd [$all get charge]"]
############################################################################33
 
I can also send you the pdb and psf file if you think you want to have a look at them.
 
Thank you!
 
 
_________________________________
Ana CÚlia Ara˙jo 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
_________________________________

 
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 CÚlia Ara˙jo Vila Verde
> Penn State University
> Department of Chemical Engineering
> Fenske Laboratory
> University Park, PA 16802
> USA
>
> < <http://www.gfct.fisica.uminho.pt/Members/acvv> 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.che.psu.edu/Faculty/JMaranas/group/avv.html
> <http://www.gfct.fisica.uminho.pt/Members/acvv> http://www.gfct.fisica.uminho.pt/Members/acvv
> _________________________________
>
>

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