VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 21 2016 - 16:54:54 CDT

Hi,
  You can load the extra parameter into one of the time-varying
per-atom "user" fields rather than the "beta" or other non-time-varying
per-atom fields. If you then create selection based on the value of "user"
or color your representations by "user" you should then be able to achieve
a variety of time-varying representations depending on the per-atom
time-varying quanities you have in your files. There are a number of
tutorials with scripting examples that you should be able to refer to,
I think Axel Kohlmeyer's tutorial is one of the better ones to refer to
for things of this sort.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 20, 2016 at 06:36:21PM +1200, Thomas Aldershof wrote:
> Hey all,
>
> I am fairly new to VMD and am just getting started with TCL scripting.
> I would like to visualise a phase change from solid to liquid with VMD, I
> already have all necessary information in a xyz trajectory file where each
> atom line has the format:
> 1 x y z q6
> Where q6 is the Steinhardt parameter I use to distinguish solid and
> liquid.
>
> I've tried storing the liquid/solid information as the element in a new
> xyz file, liquid/solid = Ag/Au. To do this, I try to follow the
> [1]A buckyball example in 5.3 of this tutorial, however it still only
> loads the element information of the first frame and it does not
> update.A I understand that this is an inherent trait of VMD, but I thought
> one could work around it with scripting.A
>
> Is there any way to update the selection/colouring by element or
> alternatively can I upload the liquid solid information straight from the
> original file with the q6 parameter.
>
> Thanks for any help you can provide,
> Thom
>
> p.s. The script file I am using, for reference:
>
> # $Id: track_element.vmd$
> set viewplist {}
> # Display settings
> display projection A Orthographic
> display nearclip set 0.000000
> display depthcue A off
> mol new {liqsol_Al6_1.xyz} type xyz waitfor all autobonds off
> animate goto 0
> mol delrep 0 top
> mol representation cpk 0.950000 0.000000
> mol color UserA
> mol selection {all}
> mol material Opaque
> mol addrep top
> mol colupdate 0 top 1
> mol scaleminmax top 0
> mol representation DynamicBonds 1.600000 0.200000 19.000000
> mol color userA
> mol addrep top
> mol rename top {Wire}
> set viewpoints([molinfo top]) {{{1.000000 0.000000 0.000000 0.000001}
> {0.000000 1.000000 0.000000 0.000000} {0.000000 0.000000 1.000000
> -0.000000} {0.000000 0.000000 0.000000 1.000000}} {{0.975860 -0.027307
> 0.216693 0.000000} {0.061060 0.986706 -0.150639 0.000000} {-0.209698
> 0.160234 0.964556 0.000000} {0.000000 0.000000 0.000000 1.000000}}
> {{0.090228 0.000000 0.000000 0.000000} {0.000000 0.090228 0.000000
> 0.000000} {0.000000 0.000000 0.090228 0.000000} {0.000000 0.000000
> 0.000000 1.000000}} {{1.000000 0.000000 0.000000 0.000000} {0.000000
> 1.000000 0.000000 0.000000} {0.000000 0.000000 1.000000 0.000000}
> {0.000000 0.000000 0.000000 1.000000}}}
> lappend viewplist [molinfo top]
> # done with molecule
> foreach v $viewplist {
> A molinfo $v set {center_matrix rotate_matrix scale_matrix global_matrix}
> $viewpoints($v)
> }
> unset viewplist
> # Set selection and obtain liquid solid classification from element
> set mol top
> set wire A [atomselect $mol all]
> set n [ molinfo $mol get numframes ]
> for {set i 0} {$i < $n} {incr i} {
> A A $wire frame $i
> A A set el_list "";
> A A # Get the element for each atom Au = solid, Ag = liquid.
> A A foreach el [$wire get {element}] {
> set sol 0
> if [ expr { $el == "Au" } ] {
> set sol 1
> }
> lappend el_list $sol;
> A A }
> #puts [ llength $el_list ]
> A A $wire set user $el_list;
> }
> animate style loop
> animate speed 0.8
> animate forward
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/Training/Tutorials/cpmd-vmd.pdf 

-- 
NIH Center 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/