Applications Based on Molecular Dynamics Methods

Theodorou and Suter have employed a chain generation scheme that works as follows  

Step 1 Generate the first three backbone atoms, including all pendant groups of the first two. Place the whole assembly in a random orientation in a box. 

Step 2 For each possible choice of the rotational state of bond i, compute the following conditional probability  

Step 3 Minimize the energy of the system while keeping bond lengths and angles constant. 

Step 3a Adjust potential energy functions to yield a soft sphere potential by halving the atomic radii from their actual size and by using no rotational barriers. 

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