VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat May 04 2013 - 00:29:25 CDT

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