VMD-L Mailing List

From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Thu Apr 02 2015 - 02:37:04 CDT

I don't know if there is a plugin for it but you could definitely write a
tcl script where for each frame you do the selection:
"water and within 2 of protein" (I don't know how far the first hydration
shell should extend so 2A might not be enough).

The you just iterate over the atomselections of each frame, group the
selected atoms by resid and whenever a resid becomes 1
(is within 2 Anstromg of protein) you count for how long the selection
stayed at 1.

On Thu, Apr 2, 2015 at 6:08 AM, M K <mahyar.karimi20_at_gmail.com> wrote:

> Hi,
>
> Does anyone know how I can calculate the residence time of water molecules
> in the first hydration layer of a solvated molecule, protein, or polymer?
>
> Thank you.
>