VMD-L Mailing List
From: Ondrej Kroutil (okroutil_at_gmail.com)
Date: Thu Oct 30 2014 - 08:49:09 CDT
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Dear VMD users,
I modified distance.tcl to get distance between water oxygen atom and
platinum atom. There is always 1 confined water molecule in the selection
but this molecule can have different id during simulation (1 water molecule
is replaced by another and so on).
First I select whole water molecule (sel2), than I get an index of OW
atom (set ndx [$sel2 list] and set ow [lindex $ndx 0]). I need to select
whole water molecule because I will need to get also distances between Pt
and HW1 and Pt and HW2.
The problem is that after processing of a script displayed below I always
get thist Pt-OW distance in the last frame for all frames:
0 3.5100714578446253
1 3.5100714578446253
2 3.5100714578446253
3 3.5100714578446253
4 3.5100714578446253
..
There is maybe problem with update of selection or variable but I cannot
find it. I'm sorry I bother you with such a easy thing. I really tried hard
to solve it by myself and but I didn't succeeded ...
Thanks a lot.
Ondrej Kroutil
********************** **********************
SCRIPT:
********************** **********************
set sel1 [atomselect top "name Pt"]
set sel2 [atomselect top "same resid as (name OW and sqrt((x-6.81)*(x-6.81)
+ (y-6.81)*(y-6.81)) < 1.2 and within 5 of name Pt)"]
set nf [molinfo top get numframes]
set outfile [open pok.dat w]
for {set i 0} {$i < $nf} {incr i} {
puts "frame $i of $nf"
$sel1 frame $i
$sel2 frame $i
set ndx [$sel2 list]
set ow [lindex $ndx 0]
set owsel [atomselect top "index $ow"]
set com1 [measure center $sel1]
set com2 [measure center $owsel]
set simdata($i.r) [veclength [vecsub $com1 $com2]]
puts $outfile "$i $simdata($i.r)"
$owsel delete
unset ow
unset com2
unset com1
unset simdata
}
close $outfile
********************** **********************
-- Ondřej Kroutil ,, Faculty of Health and Social Studies ----"))' University of South Bohemia OOO Jirovcova 24, Ceske Budejovice OOO The Czech Republic | OO E-mail: okroutil_at_gmail.com >------ O Mobile: +420 736 537 190
- Next message: John Stone: "Re: essential dynamics visualization in VMD"
- Previous message: John Stone: "Re: BUG(s): vmd-1.9.2b"
- Next in thread: Josh Vermaas: "Re: Dynamic atomselect"
- Reply: Josh Vermaas: "Re: Dynamic atomselect"
- Reply: Michał Jakub Kański: "Re: Dynamic atomselect"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]