Student Posters Repository

In order to study the dynamics of proteins and other biomolecules, we use Molecular Dynamics simulations, i.e. solving the equations of motion for systems in atomic detail with starting configurations obtained from experiments. In particular, we are interested in the gradients of free energies, as they are the universal driving forces of chemical and biophysical systems and related to fundamental processes such as binding or protein folding. Due to entropic contributions, full values of free energies can rarely be obtained, as this would require sampling the entire high dimensional conformational space. However, the difference in free energy can be determined more accurately if the phase spaces of the two states have sufficient overlap. To fulfill this requirement, we use a set of methods named Alchemical Transformations, in which simulations in intermediate states, consisting of an interpolation of the start and end states’ Hamiltonians, are conducted. We show that the choice of such pathways significantly influences the statistical accuracy of the estimates. The optimized pathways are implemented into the widely used “GROningen MAchine for Chemical Simulations” (GROMACS) open-source software package.