VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 12 2015 - 18:27:41 CDT

On Aug 12, 2015 1:56 PM, "Xiaohui She" <xshe4_at_wisc.edu> wrote:
>
> Dear all,
>
> I am using 4-site water model (O, H1, H2 and Virtual site) in my
simulation. When I visualize it with VMD, there are excess bonds (H-V and
V-O) except the O-H bond. Is there any method to delete the excess bonds
and only show the O-H bond?
>
>
> Any help will be appreciated!

You can remove them via Tcl scripting. Or you can use the dynamic bond
representation with a selection that excludesnyour virtual site.

Axel.

>
>
> Best wishes,
>
>
> Xiaohui
> University of Wisconsin-Madison
>