RE: slice of water box

From: Hongbo Du (
Date: Wed Apr 09 2014 - 20:22:04 CDT

Hi, Boshra,

If you want to calculate the interaction energies including non-bonded terms between them, you can use the Plugin NAMD Energy available in VMD based on the trajectory you have. Remember to update each frame because the movability of water molecules around the big molecule.

Good luck.
From: Boshra Moradi []
Sent: Wednesday, April 09, 2014 5:47 PM
To: Hongbo Du
Subject: Re: namd-l: slice of water box

Hi , Hongbo,
I want to survey the interactions between atoms of the main molecule and water molecules.


On Thu, Apr 10, 2014 at 3:10 AM, Hongbo Du <<>> wrote:
Hi, Boshra,

If you just want to get the coordinates of water molecules including the big molecule, you can use the ATOM SELECT method in VMD. Please check the VMD manual, it is easy to get atoms around the molecule.

Good luck,

From:<> [<>] on behalf of Boshra Moradi [<>]
Sent: Wednesday, April 09, 2014 5:13 PM
Subject: namd-l: slice of water box

I have a molecule in a water box.I want to take a slice through the box and there will be one or two water molecule layers around that molecule .How can i do it?
I will appreciate very much if
anyone can give me any advice.
Thanks in advance,

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