Miaoer Yu

Publication Date

Fall 2012

Degree Type

Master's Project


Computer Science


GROMACS is a widely used package in molecular dynamics simulations of biological molecules such as proteins, and nucleic acids, etc. However, it requires many steps to run such simulations from the terminal window. This could be a challenge for those with minimum amount of computer skills. Although GROMACS provides some tools to perform the standard analysis such as density calculation, atomic fluctuation calculation, it does not have tools to give us information on the specific areas such as rigidity that could predict the property of the molecules. In this project, I have developed a user friendly program to carry out molecular dynamics simulations for proteins using GROMACS with an easy user input method. My program also allows one to analyze the rigidity of the proteins to get its property.