VMD-L Mailing List
From: Michał Jakub Kański (michal.kanski_at_student.uj.edu.pl)
Date: Thu Oct 30 2014 - 11:49:36 CDT
- Next message: Christian Wohlschlager: "Oculus Rift"
- Previous message: John Stone: "Need testers: VMD 1.9.2 w/ interactive GPU ray tracing w/ AO, depth of field, etc."
- In reply to: Ondrej Kroutil: "Dynamic atomselect"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
After
$sel1 frame $i
$sel2 frame $i
add
$sel1 update
$sel2 update
Michal Kanski
________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Ondrej Kroutil <okroutil_at_gmail.com>
Sent: 30 October 2014 14:49
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Dynamic atomselect
Dear VMD users,
I modified distance.tcl to get distance between water oxygen atom and platinum atom. There is always 1 confined water molecule in the selection but this molecule can have different id during simulation (1 water molecule is replaced by another and so on).
First I select whole water molecule (sel2), than I get an index of OW atom (set ndx [$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<mailto:okroutil_at_gmail.com> >------ O Mobile: +420 736 537 190
- Next message: Christian Wohlschlager: "Oculus Rift"
- Previous message: John Stone: "Need testers: VMD 1.9.2 w/ interactive GPU ray tracing w/ AO, depth of field, etc."
- In reply to: Ondrej Kroutil: "Dynamic atomselect"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]