[AMBER] Creating a Gold surface library file

From: Timothy Cholko <tchol001.ucr.edu>
Date: Mon, 14 May 2018 17:35:06 -0700

I'm simulating a sensor which includes a monolayer on a flat gold
substrate. I'd like to include the flat gold surface (just 3-4 atoms thick)
but I'm having a lot of trouble creating a large enough system.

I've already accomplished this just using a few gold atoms, because I can
assign the gold atom "types" in Xleap manually, load a frcmod file for
them, and xleap will make a prmtop and rst7 for me. The problem is, I need
to simulate a surface that will have 10,000-20,000 gold atoms, so I will
not be able to assign the atom type in Xleap manually for all these atoms.

I really want to create a reusable slab of the gold surface that I can just
load multiple times and position accordingly to make a surface of a desired
size. I thought the key to doing this was to create a .lib file of the
slab, in the same way that amino acids etc. are defined in .lib files and
constructed via that template. But when I save a .lib file for a gold slab,
it seems like it only saves it as the particular object I created in that
same xleap session, and if I load an identical slab that just has different
coordinates but the same residue name, it isnt recognized and strange
things happen.

Has anyone had success with this or should I just give up on getting gold
to work in Amber? Is the .lib file the key or is there more that I need to
do to make this work?

- Tim
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Received on Mon May 14 2018 - 18:00:02 PDT
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