VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 23 2006 - 11:09:00 CDT

Hi,
  Yes, please send me your files, so I can look at them (no need to CC vmd-l
on the file send however...) Also, which version of VMD are you running?

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 23, 2006 at 12:02:14PM -0400, Ana Celia Araujo Vila Verde wrote:
> 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 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
> _________________________________
>
>
> 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> 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
> > _________________________________
> >
> >
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: <http://www.ks.uiuc.edu/~johns/> http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078