VMD-L Mailing List

From: MannyEful E (mannyeful_at_gmail.com)
Date: Tue Nov 18 2014 - 09:14:12 CST

Thanks Asasja. I thought someone would say that!
Yes I did think about this too but it's a small section of a script I'm
trying to build. I would still need to assign these values to arrays as an
input into my order parameter. And the resulting order parameter would also
need to be binned in a histogram.
On 18 Nov 2014 14:24, "Ajasja Ljubetič" <ajasja.ljubetic_at_gmail.com> wrote:

> Probably not the answer you are looking for, but my advice would be to
> write the number of waters vs timestep to a text file and do the analysis
> in Python (or R or Mathematica or whatever specialized software of your
> choice).
> When I started doing that, life became much easier:)
> Unless of course you need to display the histogram interactively etc..
>
> Best regards,
> Ajasja
>
> On 18 November 2014 14:40, MannyEful E <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)”;
>>
>> }
>>
>>
>