From: Ondrej Kroutil (okroutil_at_gmail.com)
Date: Thu Oct 30 2014 - 11:07:02 CDT

Hi Josh,

That was the problem! Thanks a lot! Now it works perfectly. I knew it! Such
a small silly mistake...
Btw. platinum doesn't move cause I have centered trajectory with still
platinum complex in the middle and water box rotating around.
Ones again thanks a lot.

Best

    OndÅ™ej

On Thu, Oct 30, 2014 at 3:55 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Hi Ondřej,
>
> I think you can fix this by changing the line:
> set owsel [atomselect top "index $ow"]
> to:
> set owsel [atomselect top "index $ow" frame $i]
>
> New atomselections default to picking the currently active frame (usually
> the last one if you don't explicitly change it with animate), so in
> principle that is at least part of the problem. Does your platinum atom
> ever move? I'm surprised to see constant distances, since if your platinum
> molecule moves at all, the distance should nevertheless change. You may
> also need to issue a $sel2 update to recalculate the atomselection at each
> frame, since in principle the water molecule nearest to the platinum atom
> is supposed to change (see the docs:
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node121.html).
>
> -Josh Vermaas
>
>
> On 10/30/2014 08:49 AM, Ondrej Kroutil wrote:
>
> Dear VMD users,
> I modified distance.tcl to get distance between water oxygen atom and
> platinum atom. There is always 1 confined water molecule in the selection
> but this molecule can have different id during simulation (1 water molecule
> is replaced by another and so on).
> First I select whole water molecule (sel2), than I get an index of OW
> atom (set ndx [$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
>
>
>

-- 
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