From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 08 2012 - 07:00:09 CDT
How should it be possible to pull a molecule out of the water, when you have periodic boundaries?
Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
From: khalil ghafarian <khalil_earth_at_yahoo.com>
Sender: owner-namd-l_at_ks.uiuc.eduDate: Mon, 8 Oct 2012 03:22:25
Reply-To: khalil ghafarian <khalil_earth_at_yahoo.com>
Subject: namd-l: Fixed atoms in SMD
I want to pull out a molecule from water box with SMD, but when I implemented SMD ,I see the whole water box move with my
molecule too , how can I keep water box fixed ?
I have used PBC and I
specified SMD atoms exactly in reference file.
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