VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 04 2005 - 10:26:53 CST

Oops, I missed seeing Axel's reply. Axel's is a more
complete answer, so I'd suggest starting with his suggestion.

  John

On Tue, Jan 04, 2005 at 08:33:53AM +0100, Axel Kohlmeyer wrote:
> 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. 

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