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