creation and equilibration of a monolayer

From: creston . (
Date: Fri Jun 20 2008 - 16:01:06 CDT

Hi All

I am new to molecular dynamics and have a few questions. I was
wondering if anyone has experience running simulations of Langmuir
monolayers in NAMD. I created the monolayer in VMD by manually
replicating phospolipids and arranging them, then solvating the
system. My first question: is there an easier way to create a
monolayer? I ran the simulation several times in NAMD with different
configurations, but none turned out the way I expected. One had
several layers of water traveling away from the main system in random
directions. Another had bizarre stretching of water molecules and
lined them up reminiscent of a chain. Does anyone know how to fix
this? If someone could send me a configuration file of a working
Langmuir monolayer I would be very appreciative.


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