VMD-L Mailing List

From: VISWANADHA SRIDHARA (vsrid001_at_odu.edu)
Date: Mon Jan 03 2005 - 18:19:04 CST

Hi Everyone,

How Can I get just the molecule ID's for a certain shape in the system?
For example, if the system is a cube of 6nm water molecules, and what
should I do to get the molecule ID's which are in say., 2nm radius from the
center of the system? I was able to get all the atoms in that specific
radii, but not just the molecules which are completely there in that
sphere.
I hope you got me.

Eg., for spc216 system

128SOL OW
128SOL HW1
128SOL HW2
129SOL OW
129SOL HW2
143SOL OW......

If you can see, for 129SOL, HW1 is out of the sphere of 2nm radius, so is
there any way to get a pdb file with just 128SOL, ignoring 129 and so on.

Thanks in advance for your help.

Vish