VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Feb 29 2012 - 16:09:59 CST

Hi,

Also, I think there is no need to create a new atom selection for each
frame (actually you create $molnumb atomselections for each frame, which
is even worse). At the very least you have to free the atom selection using
$mol_select delete or you might run out of memory.

Much better would be to create the atomselection(s) outside the loop and
then update the slection using
$mol_select frame $i
$mol_select update

Best regards,
Ajasja

On Wed, Feb 29, 2012 at 21:05, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> This command is incorrect, and is the most likely source of your error:
> set coordz [$centmas get z]
>
> Your $centmas variable is not an atom selection, but rather a vector,
> therefore this can't work the way you have written it.
> You would need to change that to something like this:
> set coordz [lindex $centmas 2]
>
> It would also help others read your script if you indented the code
> rather than writing it all starting in column zero...
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Feb 29, 2012 at 08:51:58PM +0100, vladanstefanovic_at_kg.ac.rs wrote:
> > Hello VMD users,
> >
> > I'm trying to calculate adsorption of molecules of glucose on silica
> > nanochannel wall.
> > I need to know how many molecules are adsorbed on the surface of the
> > silicate wall-SiO2 per time.
> > I made VMD Tk console script to count for each frame all molecules that
> > have coord z under min value of molecules distance from the wall; and put
> > the total number of those molecules into the array consisting of
> molecules
> > number for each frame.
> > The script doesn't work and I don't know why?
> >
> > set frmnum [molinfo top get numframes]
> > set layer_min 17.64
> > set molnumb 29
> > set counter 0
> >
> > set file_out [open Adsorption.dat w]
> >
> > for {set i 0} {$i < $frmnum} {incr i} {
> > for {set j 1} {$j <= $molnumb} {incr j} {
> >
> > set mol_select [atomselect top "segid GLUB and resid $j"]
> > $mol_select frame $i
> > set centmas [measure center $mol_select weight mass]
> > set coordz [$centmas get z]
> >
> > if {$coordz <= $layer_min} {
> > incr counter
> > }
> > }
> > set array($i.r) $counter
> > puts $file_out "$array($i.r)"
> >
> > set counter 0
> > }
> > close $file_out
> >
> > After I start the script it shows message: "invalid command name" then
> > some three numbers and stops working.
> > Can somebody please explane to me, why it doesn't work and what would be
> > the best solution.
> >
> > Best greetings,
> > Vlada
> >
> >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>