Molecular Dynamics Simulations

Molecular simulations aim to supplement the design of new peptide molecules and the prediction of their conformational landscape. The response of such molecules to various physical and chemical perturbations can also be studied. This diversity in investigation options and relatively economical execution makes simulation studies one of the most important preliminary steps in peptide design and characterization. Groningen Machine for Chemical Simulations (GROMACS) is a versatile package for performing molecular dynamics simulations and has been extensively applied for a wide variety of simulations. This protocol will support the efforts of performing molecular dynamics simulations to study peptides using the GROMACS package.