VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Tue Nov 18 2014 - 13:23:51 CST

incr hist($whichBin) -- also works.

> On Nov 18, 2014, at 12:16 PM, MannyEful E <mannyeful_at_gmail.com> wrote:
>
> Yes that's true, the corrected script is now:
>
> # Variables for Atomselection
> #set min 0 ; # lower limit of the hydration shell
> set max 3.5 ; # higher limit of the hydration shell
> set atom_ref pva5; # VMD residue name of the reference atom
>
> # Variables for Calculations
> set frame_start 0;
> set frame_end [molinfo top get numframes];
> set fp [open "hydration_number.txt" w];
> set suma 0;
>
> # Variables for Histogram
> set min_val 0;
> set max_val 100;
> set nbins 100;
> set binWidth [expr (($max_val - $min_val)/$nbins)];
>
> # initialises an array befor counting by setting all bars to zeroes
> for {set i 0} {$i < $nbins} {incr i} {
> set hist($i) 0
> }
>
> #script runs calculates the number of oxygen atoms within 3.5 of the polymer
> for {set frame $frame_start} {$frame < $frame_end} {incr frame} {
>
> # goes to the frame and updates selections
> puts "Frame $frame";
> set oxygens [atomselect top "(name OW) and (within $max of resname $atom_ref)"];
> $oxygens frame $frame;
> $oxygens update;
>
> # number of neighbouring waters, excludes itself
> set num_oxygens [$oxygens num] ;
> puts "number of oxygens is: $num_oxygens”;
>
> # sum total number of waters that have been near the polymer
> set suma [expr $suma + $num_oxygens];
> puts "current total is now: $suma”;
>
> # identifies which bin to increment
> set whichBin [expr {int ($num_oxygens - $min_val)/$binWidth}];
> puts "whichBin is: $whichBin”;
>
> set hist($whichBin) [expr $hist($whichBin) + 1];
>
> # testing print out during the loop. I get no change here
> puts "The whichBin Bin is incremented to: $hist($whichBin)";
>
> }
>
> # print out the histogram
> for {set i 0} {$i < $nbins} {incr i} {
> puts "$i $hist($i)”;
>
> }
>
> Thank you.
> On 18 Nov 2014 18:09, "Maxim Belkin" <mbelkin_at_ks.uiuc.edu <mailto:mbelkin_at_ks.uiuc.edu>> wrote:
> No problem. But check if you actually meant "num_oxygens" there - perhaps it should be "whichBin".
>
> Maxim
>
>
>> On Nov 18, 2014, at 10:15 AM, MannyEful E <mannyeful_at_gmail.com <mailto:mannyeful_at_gmail.com>> wrote:
>>
>> Thank you Maxim! :D
>>
>> On 18 Nov 2014 16:09, "Maxim Belkin" <mbelkin_at_ks.uiuc.edu <mailto:mbelkin_at_ks.uiuc.edu>> wrote:
>> Change
>> set $hist($num_oxygens) [expr $hist($num_oxygens) + 1];
>> to
>> set hist($num_oxygens) [expr $hist($num_oxygens) + 1];
>>
>>
>>> On Nov 18, 2014, at 7:40 AM, MannyEful E <mannyeful_at_gmail.com <mailto:mannyeful_at_gmail.com>> wrote:
>>>
>>> I need some advice with VMD and tcl. I am counting the number of waters around a shell of a polymer and then I want to create a histogram based on these values.
>>> I have currently obtained the value for each frame, but I’m stuck on how to increment the histogram array ($hist($i)) correctly.
>>> I can’t quite put my finger on what needs to be changed in the script below (see arrows). Any ideas??
>>>
>>> This part of the script will be important later to help me calculate the orientational order parameter of surrounding water [q=1-3/8 SUM_OVER_6_ANGLES (cos (phi_ijk) + 1/3) S. Lee et al (2005)]
>>>
>>> Thank you for your time.
>>>
>>> # Variables for Atomselection
>>> set min 0 ; # lower limit of the hydration shell
>>> set max 3.5 ; # higher limit of the hydration shell
>>> set atom_ref pva5; # VMD residue name of the reference atom
>>>
>>> # Variables for Calculations
>>> set frame_start 0;
>>> set num_steps [molinfo top get numframes];
>>> set fp [open "g_traj_hydration_vmd_3.txt" w];
>>> set frame_end $num_steps;
>>> set stride 1;
>>> set suma 0;
>>>
>>> # Variables for Histogram
>>> set min_val 0;
>>> set max_val 100;
>>> set nbins 100;
>>> set binWidth [expr (($max_val - $min_val)/$nbins)];
>>>
>>> # initialises an array befor counting by setting all bars to zeroes
>>> for {set i 0} {$i < $nbins} {incr i} {
>>> set hist($i) 0
>>> }
>>>
>>> #script runs calculates the number of oxygen atoms within 3.5 of the polymer
>>> for {set frame $frame_start} {$frame < $frame_end} {incr frame} {
>>>
>>> # goes to the frame and updates selections
>>> puts "Frame $frame";
>>> set oxygens [atomselect top "(name OW) and (within $max of resname $atom_ref)"];
>>> $oxygens frame $frame;
>>> $oxygens update;
>>>
>>> # number of neighbouring waters, excludes itself
>>> set num_oxygens [$oxygens num] ;
>>> puts "number of oxygens is: $num_oxygens”;
>>>
>>> # sum total number of waters that have been near the polymer
>>> set suma [expr $suma + $num_oxygens];
>>> puts "current total is now: $suma”;
>>>
>>> # identifies which bin to increment
>>> set whichBin [expr {int ($num_oxygens - $min_val)/$binWidth}];
>>> puts "whichBin is: $whichBin”;
>>>
>>> set $hist($num_oxygens) [expr $hist($num_oxygens) + 1]; <------
>>>
>>> # testing print out during the loop. I get no change here <-------
>>> puts "the whichBin Bin is incremented to: $hist($num_oxygens)";
>>>
>>> }
>>>
>>>
>>> # print out the histogram
>>> for {set i 0} {$i < $nbins} {incr i} {
>>> puts "$i $hist($i)”;
>>>
>>> }
>>>
>>
>