namd simulation:protein,ligand,lipid,water and ions

From: Marlet Martinez (
Date: Wed Jun 13 2012 - 18:44:40 CDT

Dear All

  I work with membrane protein NAMD simulations. My system consists of my
protein, ligand, lipid membrane, water, and ions. I have minimized my
lipid membrane and complex protein-ligand separately in order to have a
more relaxed system, and finally I could run the first configuration file
without having errors., however when I try to run the configuration file 02
my simulation automatically crashes and it does not say anything about it
(I attach log file).
I wonder if I may need to run other simulations prior to the the second
configuration file. I do not know for example if I may need a simulation to
release my ligand and then run the second (02.conf) configuration file.

I would appreciate any suggestion regarding this issue,

 Thanks in advance,


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