VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jun 02 2009 - 09:27:22 CDT

On Tue, 2009-06-02 at 09:25 -0300, Alberto Sergio Garay wrote:
> Hi

hi alberto,

> For my calculation I need to take into account the periodic boundary
> conditions of
> my system (gromacs trayectory) so I made a tcl/tk script which:
>
[...]

> Selections are clean using ?$my_sel delete?
> close the loops over frames

you may have mixed up loop nesting!
memory leaks in this kind of scripting almost
always (= 99%) are due to forgotten or
overwritten(!) selections.

> Now the problem is: the ram memory is progressively used til there's
> no left, and the pc hangs up.
> When I use a smaller trayectory (less frames) after the script
> finishes the memory is still bussy.
>
> Could anyone give any piece of advice about how to face this problem?

we need to see the script. there is no other way.

>
> I could paste the script on the mail but it is quit long, so I will
> wait for some suggestions to try before do it

_the_ way to communicate problematic or test data sets is via the
VMD public biocore project. anyone can register and join the project
(only non-public projects are hidden and need invitations). then you
can upload your files into a directory in the BioFS (best create a
subdirectory under "testfiles" and send a message to the list on
how to run your analysis, so that we can try to reproduce this.
please first make sure that your script is compatible with the
latest VMD beta release, as that would help us enormously.

thanks,
   axel.

>
> Thank you in advance.
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.