VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Tue Feb 18 2020 - 08:59:16 CST

I'd deal with this using graph theory. For each frame in your trajectory,
you'd create nodes for each molecule, and link them together if they have
contacts in that particular frame. Never done it in Tcl though, so I don't
have a script to crib off of.

-Josh

On Tue, Feb 18, 2020 at 1:36 AM Mikhail Suyetin <msuyetin_at_gmail.com> wrote:

> Dear All,
>
> Hope you are doing great.
>
> I am doing some MD simulations of SDS agglomeration in water. I have got a
> question how can I calculate how many SDS molecules per agglomerate? May be
> somebody did similar task and she/he has a tcl script?
>
> Thank you.
>
> Kind Regards,
> Mikhail
>