VMD-L Mailing List

From: MannyEful E (mannyeful_at_gmail.com)
Date: Tue Nov 18 2014 - 10:54:06 CST

Thank you Jerome, and everyone else for your help. It's running now!
On 18 Nov 2014 16:36, "Jérôme Hénin" <heninj_at_gmail.com> wrote:

> Hi,
>
> Your problem is the dollar sign right here:
> v
> set $hist($num_oxygens) [expr $hist($num_oxygens) + 1];
>
> Jerome
>
> On 18 November 2014 16:14, MannyEful E <mannyeful_at_gmail.com> wrote:
>
>> 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)”;
>>>>
>>>> }
>>>>
>>>>
>>>
>