VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Aug 16 2018 - 09:09:27 CDT

Each VMD atom selection object contains internally vectors that are as long
as the total number of atoms in the molecule, and the memory usage of these
vectors will not change with the selection keyword. I think it'd be safer
to always delete an atom selection as soon as it's not needed.

Giacomo

On Thu, Aug 16, 2018 at 10:00 AM João Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

> Also, if you need to create atom selections inside the loop (e.g. if
> zmin value changes), you should definitely delete the selection before the
> next iteration ("$sel_water($i) delete"), unless you need the atom
> selection for another operation outside the loop, or the selections don't
> take that much memory.
>
> Best
>
> João
>
> On Thu, Aug 16, 2018 at 8:14 AM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>>
>>
>> On Thu, Aug 16, 2018 at 7:17 AM fan li <fanliqmul_at_gmail.com> wrote:
>>
>>> Hi everyone
>>> I am trying to select atoms with specific region of SOL of each frame
>>> and change the selected atom's resname. I list part of my code below.
>>>
>>> ############################################
>>> set zmin 30.3
>>>
>>> set nf [molinfo top get numframes]
>>> for {set i 0} {$i < [expr (3-1)]} {incr i} {
>>>
>>> set sel_water($i) [atomselect top "resname SOL and z<$zmin"]
>>> $sel_water($i) frame $i
>>>
>>> #reset the resname of the selected water
>>> $sel_water($i) set resname den
>>>
>>> $sel_water($i) writegro "water_interest$i.gro"
>>>
>>> }
>>>
>>>
>>>
>>> ########################################
>>> This "set sel_water($i) [atomselect top "resname SOL and z<$zmin"]"
>>> selection is not working properly as the outcome is not the region I
>>> specified.
>>>
>>> Then I removed the "z<$zmin" and changed it to "set sel_water($i)
>>> [atomselect top "resname SOL"]", it woks fine as the entire water is
>>> selected.
>>>
>>> So could someone tell me why the selection is not working with the
>>> position selected condition is not working?
>>>
>>> As position selected condition changes over each frame in the actual
>>> code, so I can not put the selection outside the loop?
>>>
>>
>> that last statement is not correct something like this:
>>
>> $sel frame $i
>> $sel update
>>
>> will re-evaluate the selection stored in $sel for the frame $i (that is,
>> for as long as $zmin doesn't change, as the selection string will evaluate
>> variables when the selection is defined and not re-evaluate it when
>> updated).
>>
>> axel.
>>
>>
>>
>>>
>>> Fan
>>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> http://www.ks.uiuc.edu/~jribeiro/
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
> 

-- 
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