[gmx-users] How to performe a monolayer dynamics?

Hector Mrz-Seara Monne hseara at netscape.net
Wed Sep 22 16:59:18 CEST 2004

First of all, let me thank in advance,

After reading several references about monolayers , and bilayers 
specially those performed by Erik Lindal and Peter Tieleman there are 
several things that worry me. My system isn't a tipical lipid monolayer, 
it is contituted by hydrocarbonated-azo-benzene with a carboxylated head 
and to start we want to reproduce an experimental isoterm.

 I have charge the carboxylix acid at the end of the chain and then when 
I made the monolayer and run the dynamic without water, the monolayer is 
destroyed by the coulomb forces, as I expected.  But as I read many 
authors said that they start the simulation without water to allow the 
monomer to get a better tilt of chains. How they perform that? How were 
they able to maintain the heads at z=0 for afterwards insert the waters 

Another question is that, as I know the best way of calculating couloumb 
forces is with PME in gromacs. That is true? Why then lots of people 
using gromacs use a shifted cut-off? In case of using PME I have to 
neutralize my system with ions ( in the hydrated monolayer)?, and in the 
case of using a cut-off?

Thank you.
Hector Martínez-Seara Monné

Universidad Barcelona
Dpt. Química-Física

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