AW: Drifting water molecules

From: Norman Geist (
Date: Thu Nov 28 2013 - 02:59:56 CST

Use vmd to wrap the trajectory and save a new dcd.


Norman Geist.


Von: [] Im Auftrag
von Axel Kohlmeyer
Gesendet: Mittwoch, 27. November 2013 23:56
An: Mihaela Drenscko;
Betreff: Re: namd-l: Drifting water molecules


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


Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.
From: Mihaela Drenscko <> 
Date: Wed, 27 Nov 2013 17:45:10 -0500
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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