VMD-L Mailing List

From: Jawahar Neelankatan (neelankatan_j_at_yahoo.com)
Date: Fri Mar 02 2007 - 06:19:38 CST

Hi all,
In order to save memory and avoid using the atomselect command for each frame in a trajectory, I usually do the atomselection at the beginning and use either "$sel frame $i" or "$sel update" to update the atomselection for each frame.
My question is this: exactly how does the update process work ? My guess is that if X atoms are selected in the initial atomselect command, the "update" command updates the coordinates of those X atoms in each new frame.
So, if the atomselect command has a selection criterion such as "within 12 of ion", then all atoms within a sphere of radius 12 Angstrom around the ion are selected. Let's assume there are X atoms fitting this criterion, in the first frame. When the frame is switched to another frame and the "update" command is used, is it those same X atoms that are updated, or is the atomselection command repeated for that particular frame ? My concern is that, in the new frame, an atom that was previously within the 12 Angstrom sphere might have moved out of the sphere, so it is pointless to update its coordinates.

-Jawahar.

 
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