VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Apr 11 2023 - 16:16:29 CDT

Hi, the simplest way to achieve this would be to treat the Cl- atoms
independently, i.e. create one DynamicBonds representation between the La+
ion and *only one* of the Cl- ions, and then repeat this step for the
others. A Tcl loop would be best to save manual writing.

Giacomo

On Tue, Apr 11, 2023 at 5:05 PM Rajorshi Chattopadhyay <
rajorshichat_at_gmail.com> wrote:

> Dear all,
>
> I am trying to make a visualisation of my simulation trajectory that
> contains La, Cl ions in an aqueous solution. I want to draw bonds
> between the La and those Cl ions which are in the first coordination shell,
> for all the frames.
>
> I tried this out by creating two separate groups of atoms, one
> containing the La ion and the other containing the coordinating Cl ions. I
> have then used the DynamicBonds drawing method to draw bonds between the
> two groups. I find that this creates bonds correctly between the La ion and
> Cl ions, but extra bonds between the Cl ions that are within the set cutoff
> are also drawn. Relevant portion of the tcl script is as follows:
>
> atomselect macro hyd {name H}
>
> atomselect macro oxy {name O}
>
> atomselect macro cl {name Cl}
>
> atomselect macro na {name Na}
>
>
> atomselect macro clcoord {cl within 3.8 of name La}
>
>
> mol representation VDW 0.500000 21.000000
>
> mol color Name
>
> mol selection {name La}
>
> mol material Opaque
>
> mol addrep top
>
>
> mol representation VDW 0.300000 20.000000
>
> mol color Name
>
> mol material Opaque
>
> mol selection {clcoord}
>
> mol addrep top
>
> mol selection {name La or clcoord}
>
> mol representation DynamicBonds 3.50000 0.150000 15.000000
>
> mol addrep top
>
>
> Is there a way to remove these extra bonds between the Cl ions ? I thank
> you in advance for your help/suggestions.
>
>
> --
> With Regards,
> Rajorshi Chattopadhyay,
> PhD Researcher in Mineralogy/Crystallography,
> Institut für Geologie und Mineralogie,
> Universität zu Köln, Germany
>
>