From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Nov 28 2013 - 02:59:56 CST
Use vmd to wrap the trajectory and save a new dcd.
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.
-- 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 --- Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv. http://www.avast.com
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