Hello,
I am working on molecular dynamics to find out the interaction energies between the drug molecule and alloy. My process involves following steps

1. Making of alloy (Thanks to Dr. DeJoannis) and then the alloy crystal was cleaved along the required face of the crystal to a depth of one-unit cell, and the surface was expanded to 6*6 cells in two dimensions and converted into an integral superlattice.
2. Then energy minimized drug molecule is properly positioned above the alloy superlattice with its closest atom(s) approximately 2 A ° away from the surface, it was rotated about the x, y, and z-axes to generate eight different initial orientations without changing its minimized molecular geometry.
3. Then molecular dynamics was carried out for each initial orientation at 300 K and constant volume with a time length of 1 ps.

I need help in creating a script so that above mentioned second and third step can be automated. It is because manually changing the distance between the surface of superlattice and drug molecule may change the geometry, inaccuracy in placing drug molecule at an exact distance as well as in rotation of drug molecule at a different orientation.  

I am at the basic level of using this software that is the reason I am unable to make a script on my own. However, I would like to explore its different application which can be useful in pharmaceutical industry, especially in solid dosage forms development and manufacturing.

Thank You.
Kaushalendra Chaturvedi