This was my masters(Physics) project work done at Indian Institute of Technology - Madras in May-1998. Here I have worked on protien folding problem and have done analysis to see how does a molecule made of hydrophobic and hydrophillic parts changes it's shape when put into an aquous medium. For example if we have a molicule made up of alternate hydrophobic and hydrophillic parts, the molicule entangles and changes shape in such a way that hydrophobic components lie inside and hydrophillic components lie outside the newly formed mmolicule. The software program is written to simulate the whole process so that you can see it actually changing shape. The code will be available sometime later, however here is Project Report for now.