AMBER Archive (2003)

Subject: AMBER: problem regarding surface

From: Vikas Varshney (vikas_var_at_rediffmail.com)
Date: Wed Aug 06 2003 - 12:00:09 CDT

Hi,
I am Vikas. I am persuing my graduate studies at University of
Akron in Department
of Polymer Science. My research is related to molecular dynamics
simulations of
adsorption of polymers at alumina(Al203) surface and I am using
AMBER-7 for these
simulations. When I started building the surface, I got stuck into
some problems
which I am writing below.

1. The alumina is inorganic material so I do not have force field
parameters for that. I
do not know how to get those parameters for alumina ( Aluminum and
Oxygen). I
have the co-ordinates of aluminum and oxygen atoms with me as I
have full
specifications of Alumina crystal. I do not know how to calculate
the charges and
vanderwall's parameters for the Aluminum and Oxygen atoms in the
crystal. Further,
this would be a surface so all the atoms would be fix. So I am
wondering what all
parameters would be necessary for me to build alumina surface.

  2. Since I am working on surfaces, my box would only be periodic
in two
dimensions. I do not know how to incorporate two dimensional
periodicity instead of
three for simulation box. Please help me with this if anybody know
about this.

  Regards,
  Vikas

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