Re: Drifting water molecules

From: Axel Kohlmeyer (
Date: Wed Nov 27 2013 - 16:56:17 CST

Sounds like your analysis program is broken and cannot properly handle periodic boundary conditions.


Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.
-----Original Message-----
From: Mihaela Drenscko <>
Sender: owner-namd-l_at_ks.uiuc.eduDate: Wed, 27 Nov 2013 17:45:10 
To: <>
Subject: namd-l: Drifting water molecules
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,

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