From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 27 2013 - 16:56:17 CST
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. -----Original Message----- From: Mihaela Drenscko <quo.physics_at_gmail.com> Sender: owner-namd-l_at_ks.uiuc.eduDate: Wed, 27 Nov 2013 17:45:10 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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