From: arash azari (
Date: Thu Nov 10 2011 - 07:58:28 CST

Dear all,

I would like to know extra options for pbwithin selection in atomselect.
Could you please let me know (by using pbwithin) how can I select all
the water molecules in all image cells, not only 26 cells?
How can I use the option “numperiodic” in atomselect?
For more information please read the following lines.
Thank you,


For example whenever I am saying to VMD to select:
“name OH2 and pbwithin 5 of protein” and then loop over 40 ns of my
simulation length to get the pdf files for each frame, it returns e.g.
12000 atoms for the first frame and it ends up with 7000 atoms for the
last frame; my system leaks!
When I checked my system in VMD and used the selection command in
graphical representation GUI, I noticed that pbwithin only selects the
atoms in the adjacent image cells (a cube with 27 cells which the
central one is our original cell, say 26 image cells for selection),
but I have so many water (oxygen) molecules which are located outside
these image cells and pbwithin does not select them.
I know one way is using PBCTools and wrap everything within the
original cell, but I would like to avoid this option, because I am
calculating the diffusion coefficient (MSD) for water molecules and I
cannot use the wrap command.
Another way is by writing a painful code (my system is slightly large;
around 500,000 atoms) which selects all the water molecules and makes
an imaginary protein coordinates in all image cells and then
calculating the distance from protein and making selection and getting

Arash Azari