VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue Jan 04 2005 - 01:33:53 CST

On Mon, 3 Jan 2005, VISWANADHA SRIDHARA wrote:

hi vish,

to achieve your goal, you have to create a selection for the
water oxygens only and combine that with a selection for the hydrogens
around those oxygens. e.g. if the atom with index 0 is your reference
point, it would look like this.

"(name OW and within 20.0 of index 0)
or (name HW1 HW2 and within 1.2 of (name OW and within 20.0 of index 0))"

this can be made more readable through the use of macros. see
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part4.html#chap6_sect1
for a more elaborate example for multiple solvation shells around ions.

axel.

VS>
VS> Hi Everyone,
VS>
VS> How Can I get just the molecule ID's for a certain shape in the system?
VS> For example, if the system is a cube of 6nm water molecules, and what
VS> should I do to get the molecule ID's which are in say., 2nm radius from the
VS> center of the system? I was able to get all the atoms in that specific
VS> radii, but not just the molecules which are completely there in that
VS> sphere.
VS> I hope you got me.
VS>
VS> Eg., for spc216 system
VS>
VS> 128SOL OW
VS> 128SOL HW1
VS> 128SOL HW2
VS> 129SOL OW
VS> 129SOL HW2
VS> 143SOL OW......
VS>
VS> If you can see, for 129SOL, HW1 is out of the sphere of 2nm radius, so is
VS> there any way to get a pdb file with just 128SOL, ignoring 129 and so on.
VS>
VS> Thanks in advance for your help.
VS>
VS> Vish
VS>
VS> 

-- 
=======================================================================
Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.