VMD-L Mailing List

From: Alberto Sergio Garay (sgaray_at_fbcb.unl.edu.ar)
Date: Tue Jun 02 2009 - 07:25:16 CDT

Hi

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:

loops over frames:

        selects the atoms which are close to my target residue but not in the
central box.
        moves the atoms to the new location, applying the appropriate translations.
        selects again the atoms within a radio which are ?now? physically
close to the target.
        Starts the calculation (water bridges between some of the selected
atoms). This part of the script was taken from the the tcl/tk script
of Dr. Andriy Anishkin which it worked fine alone.

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

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?

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

Thank you in advance.