Re: Fixed atoms in SMD

From: Axel Kohlmeyer (
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
International Centre for Theoretical Physics, Trieste. Italy.

-----Original Message-----
From: khalil ghafarian <>
Sender: owner-namd-l_at_ks.uiuc.eduDate: Mon, 8 Oct 2012 03:22:25
Reply-To: khalil ghafarian <>
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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