The last century has been encompassed with the development of numerous experimental methods that help us understand the human body better. Proteins are one of the key functional units in our bodies that make us who we are and allow us to perform the functions we can. the indispensable role of proteins can be actively seen during information transmission and metabolism. Traditionally, while studying a protein structure, an investigational study starts with constructing a logical hypothesis, followed by theoretical predictions and experiments, that then provides us with the experimental results. These experiments are executed multiple times to have enough dare ta for comparison and improvement of the model. In the past decade, the development of information technology and in-silico methods, we have been able to optimize the traditional experimental technique by formulating a model, performing simulations, and obtaining the simulation results that can then be compared with previously available data to predict protein structures.
Introducing GROMACS to the Scientific Community
GROMACS is an open-source software that is used to perform molecular dynamics simulations and energy minimization. Molecular dynamics simulations run on techniques that help us effectively understand and predict the structures and functions of a macromolecule based on the available information on an atomic level. Primarily, GROMACS is used to observe motions and dynamics of proteins.
Molecular dynamics work is entirely based on the models obtained from the similarity analysis of structural and chemical data.
GROMACS allows the potential models to move and adapt in more favorable conformations, enriching the detection of protein-protein interactions.
References
Metzler, Ralf. 2018. “Viewpoint: The Dance of Water Molecules around Proteins.” Physics 59.