VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Jan 27 2017 - 02:01:13 CST

Hi Alexander,

I am not sure about the two lines of code you are using as in their
objective.

>From the post script what I get is that you couldn't load the entire
trajectory in one go because of memory issues.
A workaround to do that is to load lesser frames from your trajectory -- or
maybe think about deleting the solvent. If you don't load the solvent, you
trajectory should become manageble (unless its not tooooo long). Another
workaround is to load specific frames. e.g. if you trajectory has 100
frames you can load every 3rd frame and end up with say 33 frames equally
spaced along the length of the trajectory. Usually consecutive frames are
too related anyway to infer useful information (my take). Loading frames
with a little gap can give you a workaround.

If stripping the trajectory of waters works for you (assuming you system
has waters - or anything unnecessary) and your trajectory remains big - you
can then load frames at intervals.

to jump frames -- use

first ?? *step ??* last ?? waitfor all 0

to strip the trajectory of something -- use catdcd available here :
http://www.ks.uiuc.edu/Development/MDTools/catdcd/

Looking at your code again -

I wonder if you are making selections ... if you make selections in VMD
using atomselect - are you deleting those selections?
VMD/TCL has this thing where a selection keeps occupying the memory and
doesn't release it.

to do this if you make a selection like

set sel [atomselect top all]
--- do something with selection *"sel" *---
$sel delete

by using delete - you should be able to free the space. (just throwing this
in there if this is the issue).

Hope one of these works for you. If it doesn't write back.

Best,
/A

On Fri, Jan 27, 2017 at 11:03 AM, Alexander Balaeff <abalaeff_at_gmail.com>
wrote:

> Dear VMD community:
>
> Could anyone possibly suggest a workaround of VMD running out of
> memory due to (suspected) multiple file opening? In the attached
> script, I am repeatedly reading frames from a DCD file(*) using mol
> addfile; basically, with this sequence repeated in two nested loops:
>
> animate delete all 0
> mol addfile $dcd_file(0) first $i last $i waitfor all 0
>
> End result: VMD (LINUXAMD64 version 1.9.2beta1) runs out of memory. I
> see nothing else in the script that could cause it and suspect the
> issue is VMD running afoul of the TcL file handling: opening the same
> file multiple times, growing some intrinsic buffers for file reading,
> etc., etc.
>
> Has anyone encountered similar issues? Would using animate read
> instead of mol addfile work better? Any suggestion would be greatly
> appreciated.
>
> Best,
>
> Alexander.
>
> (*) The reason I am doing so is that the whole DCD file wouldn't fit
> to the memory and I want to avoid reading it by pieces and then
> stitching the results together.
>
> =====================================================
>
> Prof. Alexander Balaeff
>
> University of Central Florida
> NanoScience Technology Center
> 12424 Research Parkway, Suite 400
> Orlando, FL 32826
>
> Phone: (407) 823-4576
> FAX: (407) 882-2819
> E-mail: abalaeff_at_gmail.com
> 

-- 
Best,
/A