VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat May 04 2013 - 08:36:41 CDT

Ah, it's just a visualization issue - your waters are definitely not flying
away. For some unknown reason, in the example configuration, wrapWater is
off. Try changing it to wrapAll on.

-----Original Message-----
From: Maximilian Ebert [mailto:m.ebert_at_umontreal.ca]
Sent: Saturday, May 04, 2013 9:32 AM
To: JC Gumbart
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: ABF tutorial: Methane-Hydration water going -> Water in
gas phase?

This is the tutorial config which I use and still water molecules are
leaving the water box in the x and y coordinate. The volume is not constant
with this configuration. Any idea why?

Max

On 2013-05-04, at 1:29 AM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> You should be running constant volume, not constant pressure. See the
> example configuration file provided:
> http://www.ks.uiuc.edu/Training/Tutorials/namd/ABF/ABF-tutorial-files/
> Methan
> e-Hydration/ABF/abf_window1.conf
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
> Behalf Of Maximilian Ebert
> Sent: Friday, May 03, 2013 10:14 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: ABF tutorial: Methane-Hydration water going -> Water
> in gas phase?
>
> Hi there,
>
> I made a mistake in my previous post. I meant that the water molecules
> expand in x and y coordinates so that after the first step the water
> box is not 30x30x30 anymore but 120x120x30. Did anybody see the same?
> Is the normal? I thought the water box needs to have the same size all
> the time to have the same water concentration during the simulation.
>
> Thank you!
> Max
>
>
>