VMD-L Mailing List

From: Maximilian Ebert (m.ebert_at_umontreal.ca)
Date: Sat May 04 2013 - 08:32:23 CDT

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
>
>
>