
CHARMM force field parameters have been recently developed for
silicates and aluminumsilicates.  This document shows how to set up
input files for a slab of (011) quartz surface, taking advantage of
the ability of CHARMM to perform MD simulations of peridic systems.

Pedro Lopes and Alexander D. MacKerell, Jr.

An auxiliary program, patchfind, has been developed to help in the
definition of the patches between atoms in the primitive cell and
neighbouring cells. Lists of bonds, angles and dihedrals, with the
assignment of atoms along particular directions, are produced.  You
can find patchfind.x in ./code directory.

The topology and parameter file is in the ./toppar subdirectory

Steps for successful use of silicates and aluminumsilicates parameters
in modeling surfaces:

1) Primitive unit cell of the surface in XYZ format (input.xyz): the
surface has to be oriented along the X-Y plane. X is made to
correspond to the crystalline a-vector and Y to the crystalline
b-vector. c is orthogonal to a and b.

2) crystal.dat file: contains the a, b, c, alpha, beta and gamma
crystal parameters:

7.3000
4.9100
44.5000
90.0
90.0
109.6517

3) run the program patchfind.x: if no mistakes were made it produces a
list of bonds, angles and torsions that can be used to define the
patches between the primitive and neigbouring cells. Common mistakes
are made in the definition of the crystal parameters.  The space is
divided according to the following drawing.  The priminitve cell is
always 1. Replica along the a-vector is refered as XX or 2 and replica
along the b-vector is refered as YY or 3. XY or 4 is the cell
resulting from a+b.

To run patchfind.x  ./code/patchfind.x > patches.dat

-----------------------
|          |          |
|    3     |     4    |
|   YY     |    XY    |
|          |          |
-----------------------
|          |          |
|    1     |     2    |
|Primitive |    XX    |
|          |          |
-----------------------

Example output is:

Torsions along XX and YY
   17    1    9   25      3  1  1  2
   18   22   30   27      2  1  1  3
 
In this case both torsions span tree cells: primitive, XX and YY.

With this information the creation of the topology file is
straightforward.

4) Create topology file: an example for quartz (011),
is available in ./toppar/top_silicates.inp

5) A CHARMM input file, test.inp, is included. It reads the primitive
cell, replicates 8x5 times the primitive cell to create the unit cell,
then generates the images and patches the images. Required files are
top_silicates.inp, par_silicates.inp, params.str, crystal.img and
image_patch.str.


