VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Mon Jul 19 2004 - 04:09:34 CDT

hi everybody,

i am having a little problem visualizing solvation shells
in an electrolyte solution. an example snapshot of the best
i could come up with so far is attached. perhape some of
you have a better idea to tackle this.

you can see the sodium and and chlorid ions, their surrounding
water molecules and the structure of the solvation shell should
be emphasized via the transparent light blue and green dynamic
bonds. also solvent separated and contact pairs are shown by
the white and yellow bonds, but that does not matter here.

what i am looking for, is a way to aviod the dynamic bonds
between the water oxygens. especially with the chloride ions,
where the oxygen-anion distance is quite large compared to the
oxygen-oxygen distance. but occasionally i also get those unwanted
and distracting bonds around the cations as well.

the relevant VMD code to create the visualizations is:

mol representation VDW 0.500000 20.000000
mol color Name
mol selection {name Na}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol representation VDW 0.500000 20.000000
mol selection {name Cl}
mol addrep top
mol selupdate 1 top 0
mol representation CPK 1.400000 0.900000 10.000000 6.000000
mol selection {same residue as (name OW and within 2.8 of name Na)}
mol addrep top
mol selupdate 2 top 1
mol representation DynamicBonds 2.800000 0.200000 10.000000
mol color ColorID 15
mol selection {(name OW and within 2.8 of name Na) or name Na}
mol material Transparent
mol addrep top
mol selupdate 3 top 1
mol representation CPK 1.400000 0.900000 14.000000 6.000000
mol selection {same residue as (name OW and within 4.0 of name Cl)}
mol material Opaque
mol addrep top
mol selupdate 4 top 1
mol representation DynamicBonds 4.000000 0.200000 10.000000
mol color ColorID 12
mol selection {(name OW and within 4.0 of name Cl) or name Cl}
mol material Transparent
mol addrep top
mol selupdate 5 top 1
mol representation DynamicBonds 6.000000 0.300000 10.000000
mol color ColorID 8
mol selection {name Na or name Cl}
mol material Opaque
mol addrep top
mol selupdate 6 top 0
mol representation Lines 1.000000
mol color Name
mol selection {all}
mol addrep top
mol selupdate 7 top 0
mol representation DynamicBonds 3.000000 0.500000 10.000000
mol color ColorID 4
mol selection {name Na or name Cl}
mol addrep top
mol selupdate 8 top 0

does anybody have a better idea besides recalculating and
setting all dynamic bonds manually via tracing vmd_frame
and 'atomselect setbonds'?

TIA,
        axel. 

-- 
=======================================================================
Dr. Axel Kohlmeyer                        e-mail: axel.kohlmeyer_at_rub.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/
=======================================================================

nacl solvation shells