Drift of the center of mass of lipid bilayer

From: Dai, Jian1 (jian1.dai_at_ttu.edu)
Date: Mon May 24 2010 - 13:26:39 CDT

Hi, NAMD users:
I have built up a membrane and peptide (melittin monomer) system. Basically I'm following the steps and using the configuration files from the NAMD membrane protein tutorial.
The system looks fine to me in the equilibration stages until the long production run. The center of mass of the lipid bilayer as well as the inserted peptide seems to drift downward.
The .conf file for production is attached.
The snapshots of the system at the beginning and at 11 ns can be seen at:
http://s663.photobucket.com/albums/uu358/djpittdj/?action=view&current=start.png
http://s663.photobucket.com/albums/uu358/djpittdj/?action=view&current=end.png
Can anyone give us some suggestions?
Thank you in advance.
Jian


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