
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. 

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.

Example topology 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), top_quartz_011.inp, is available in ./toppar

5) A CHARMM input file, test.inp, is included. It reads the unit cell, obtained by replicating 8x5 times 
the primitive cell, generates the images and patches the images. Required files are top_quartz_011.inp, 
par_silicates.inp, params.str, crystal.img and image_patch.str. 












