VMD-L Mailing List

From: Udaya Dahal (dahal.udaya_at_gmail.com)
Date: Fri Apr 27 2018 - 09:21:39 CDT

If you want to delete all atom selection after each run, just use
foreach sel [atomselect list] {$sel delete}

otherwise you have to explicitly delete variables as Brian mentioned.

Regards,

On Fri, Apr 27, 2018 at 9:59 AM, Brian Radak <brian.radak_at_gmail.com> wrote:

> +1 to Giacomo.
>
> For the record (although you should really read the documentation!) the
> syntax for deleting a selection freeing up memory is:
>
> <selection value> delete
>
> as in this pseudocode:
>
> set compare [atomselect top "residue 1"]
> for # iterate frames {
> $compare frame $frame
> <measure>
> }
> $compare delete
>
> I would hazard a guess that VMD attempts to clean up all such objects
> whenever it exits, but it will almost always be much better to delete them
> explicitly.
>
> On Fri, Apr 27, 2018 at 8:01 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Any atom selection created in VMD will take up memory. I'm not sure if
>> that's the cause in your case (how many POPC molecules are there?), but you
>> should remove the selections that you don't use any more. The
>> documentation of the atomselect command contains the syntax for that.
>>
>> Also, the "get" method for an atomselection returns the requested
>> property for each atom in the selection. Try printing the result of "get
>> residue".
>>
>> Giacomo
>>
>> On Fri, Apr 27, 2018 at 12:30 AM, Sadegh Faramarzi Ganjabad <
>> safaramarziganjabad_at_mix.wvu.edu> wrote:
>>
>>> Hello all,
>>>
>>> I am trying to calculate RMSD of individual lipids in a protein-lipid
>>> system. I found this code that aligns a single residue and gets the RMSD of
>>> the entire trajectory.
>>>
>>> # Prints the RMSD of the protein atoms between each timestep
>>> # and the first timestep for the given molecule id (default: top)
>>> proc print_rmsd_through_time {{mol top}} {
>>> # use frame 0 for the reference
>>> set reference [atomselect $mol "residue X" frame 0]
>>> # the frame being compared
>>> set compare [atomselect $mol "residue X"]
>>>
>>> set num_steps [molinfo $mol get numframes]
>>> for {set frame 0} {$frame < $num_steps} {incr frame} {
>>> # get the correct frame
>>> $compare frame $frame
>>>
>>> # compute the transformation
>>> set trans_mat [measure fit $compare $reference]
>>> # do the alignment
>>> $compare move $trans_mat
>>> # compute the RMSD
>>> set rmsd [measure rmsd $compare $reference]
>>> # print the RMSD
>>> puts "RMSD of $frame is $rmsd"
>>> }
>>> }
>>>
>>>
>>> but when I iterate this code for all lipid residues it takes a lot of memory and my computer freezes. I'm not sure why. Here is the code I'm using
>>>
>>>
>>>
>>> set selmode [[atomselect top "resname POPC"] get residue]
>>> #gets stdin selmode
>>> foreach r $selmode {
>>>
>>> # selection
>>> set reference [atomselect top "residue $r" frame 0]
>>> set compare [atomselect top "residue $r"]
>>> set num_steps [molinfo top get numframes]
>>> set output [open "rmsd_$r.dat" w]
>>> # rmsd calculation loop
>>> for {set frame 0} {$frame < $num_steps} {incr frame} {
>>> # get the correct frame
>>> $compare frame $frame
>>>
>>> # compute the transformation
>>> set trans_mat [measure fit $compare $reference]
>>> # do the alignment
>>> $compare move $trans_mat
>>> # compute the RMSD
>>> set rmsd [measure rmsd $compare $reference]
>>> # print the RMSD
>>> #puts "$r"
>>> puts $output "$rmsd"
>>> }
>>>
>>> close $output
>>>
>>> }
>>>
>>>
>>>
>>> Does anybody know a better way of doing this?
>>>
>>> Thanks,
>>> Sadegh Faramarzi,
>>>
>>> Research Assistant
>>> West Virginia University, Department of Chemistry
>>> Email:safaramarziganjabad_at_mix.wvu.edu
>>>
>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>