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

From: Maxim Belkin (
Date: Tue Jul 08 2014 - 18:40:15 CDT

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.


On Jul 8, 2014, at 6:20 PM, Thomas Evangelidis <> wrote:

> Greetings,
> Is anyone aware of any tool that helps visualize and/or quantify the flow of water into a transporter from an MD trajectory? I have a long trajectory of a transporter and want to find the main entrance points of water. I can see by manual inspection the various entrance points but it is difficult to decide which is/are the most important.
> thanks,
> Thomas
> --
> ======================================================================
> Thomas Evangelidis
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> email:
> website:

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