AW: Drifting water molecules

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.

 

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
---
Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv.
http://www.avast.com

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:57 CST