VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Aug 19 2008 - 15:14:42 CDT

On Tue, 19 Aug 2008, Emily Moore wrote:

EM> Thanks for the help. I was afraid that was the case. I'm aware of the gofr

emily,

it is not that difficult. here is the solution to the problem i was
working on today. i have coordinates of special particles (X) that
are computed from the electronic structure and an additional parameter
in a file WANNIER_CENTER. the additional parameter is is column 5.

  package require pbctools
  set mol [mol new linh3-wc.psf waitfor all]

  mol addfile IONS+CENTERS.xyz waitfor all
  pbc set {14.831 14.831 14.831} -all
  pbc join bonded -all
  set xsel [atomselect $mol "name X"]
  set nf [molinfo $mol get numframes]
  set nx [$xsel num]
  set fp [open WANNIER_CENTER r]
  for {set f 0} {$f < $nf} {incr f} {
    set ul {}
    for {set i 0} {$i < $nx} {incr i} {
      gets $fp line
      lappend ul [lindex $line 4]
    }
    $xsel frame $f
    $xsel set user $ul
  }
  close $fp

i'm loading this script and then can go on with visualization
or analysis by using selections of the kind "name X and user > 3.0"

EM> issues and I'm using the alpha test build for my calculations.

ok. great. i saw you use a very large cutoff.
are you by any chance working with valeria?

cheers,
   axel.

EM>
EM> Thanks again,
EM> Emily Moore
EM>
EM> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.