From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Nov 28 2013 - 04:17:47 CST
Won't help, if the analysis code is not PBC aware.
Axel.
--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
-----Original Message-----
From: "Norman Geist" <norman.geist_at_uni-greifswald.de>
Date: Thu, 28 Nov 2013 09:59:56
To: <akohlmey_at_gmail.com>
Cc: Namd Mailing List<namd-l_at_ks.uiuc.edu>
Subject: AW: namd-l: Drifting water molecules
Use vmd to wrap the trajectory and save a new dcd.
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Axel Kohlmeyer
Gesendet: Mittwoch, 27. November 2013 23:56
An: Mihaela Drenscko; namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: Drifting water molecules
Sounds like your analysis program is broken and cannot properly handle
periodic boundary conditions.
Axel
--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
_____
From: Mihaela Drenscko <quo.physics_at_gmail.com>
Sender: owner-namd-l_at_ks.uiuc.edu
Date: Wed, 27 Nov 2013 17:45:10 -0500
To: <namd-l_at_ks.uiuc.edu>
Subject: namd-l: Drifting water molecules
Hi,
When I run water on graphite simulation, my water bulk drifts towards next
cell, such that at the end of the simulation I have part of the water in one
cell and part in another.
I have to do an analysis of the trajectories and the program I use does not
read the part of the water molecules that are in the adjacent cell.
What can I do to keep all water molecules centered in one cell, such that
my program can read all trajectories?
Thank you,
Mihaela
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