Re: how to quantify and visualize the flow of water into a protein

From: Thomas Evangelidis (
Date: Tue Jul 08 2014 - 19:04:01 CDT


I thought about water density too, but it doesn't give you much information
about water influx. Water is always present at the entrance points but gets
in and out spontaneously. This is not captured by water density.
Στις 9 Ιουλ 2014 2:40 ΠΜ, ο χρήστης "Maxim Belkin" <>

> Hi Thomas,
> This question is not really related to NAMD. A better place for 'analysis'
> type of questions is VMD mailing list.
> Anyway, If your trajectory fits into RAM, you can use VMD volmap plugin to
> compute water density distribution averaged across the entire simulation.
> However, manual scripting might be required if "entry points" move around--001a11c33fcc113bbb04fdb772d2--

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