[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?
Hector Martínez-Seara Monné
More information about the gromacs.org_gmx-users