VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Mon May 16 2016 - 13:53:54 CDT

That still doesn't sound problematic to me. Does the screen freeze (i.e.
does it hang)? And what about the output file it creates? Is that totally
blank?

On Mon, May 16, 2016 at 1:57 PM, Dive, Aniruddha Mukund <
aniruddha.dive_at_wsu.edu> wrote:

> Hi Chitrak,
>
>
> When I load the tcl file it does nothing, does not give me any errors nor
> does it run and creates an output file. The tcl window remains blank.
>
>
> Regards,
>
> *Aniruddha M Dive*
>
> PhD student
>
> School of Mechanical and Materials Engg.
>
> Washington State University
>
>
> ------------------------------
> *From:* Chitrak Gupta <chgupta_at_mix.wvu.edu>
> *Sent:* Monday, May 16, 2016 9:30 AM
> *To:* Dive, Aniruddha Mukund
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: TCL script to track molecules moving within a
> specified region each time frame
>
> Hi Aniruddha,
>
> When you say "the script is not working", what does it do? Does it give an
> error? If not, what is it?
> 
>
> Best,
> Chitrak.
>
> On Mon, May 16, 2016 at 3:52 AM, Dive, Aniruddha Mukund <
> aniruddha.dive_at_wsu.edu> wrote:
>
>> Hi,
>>
>>
>> I want to track the molecules moving through a specific region of my
>> simulation box and save the trajectory of those molecules in a .gro format.
>> I am currently using a below tcl script for the same.
>>
>>
>> set distance 5
>> set nearby [atomselect top "chain G and name C1 O2 and within $distance
>> of name CA"]
>> set nf [molinfo top get numframes]
>> set file [open "dump_dol.gro" w]
>> for {set frame 0} {$frame < $nf} {incr frame 1} {
>> $nearby frame $frame
>> $nearby update
>> puts $file [$nearby get {x y z}]
>> puts $file "\n"
>> }
>> close $file
>>
>>
>> But the above script is not working even though the atom selection works
>> perfectly, how do I write the required output trajectory file ?
>>
>>
>> Kindly help with this issue??
>>
>>
>> Thanks,
>>
>> *Aniruddha M Dive*
>>
>> PhD student
>>
>> School of Mechanical and Materials Engg.
>>
>> Washington State University
>>
>
>