One of my research interests is how different solvation or electrostatic models influence the results of molecular dynamics calculations. As an example, I have investigated the protein ubiquitin that due to its small size allows the calculation of lng trajectories in a reasonable amount of computer time. To simulate the effect of the surrounding solvent, one can use either a periodic box or a small shell of explicit water molecules around the biomolecular system. Another important issue is the treatment of the long-range electrostatic interactions during such a MD simulation. Here, using an Ewald summation scheme leads to trajectories that stay much closer to the initial protein crystal structure than conventional cutoff schemes. Another project was the calculation of the free energy difference of the two anomeric forms of glucose. After a careful derivation and calibration of the necessary parameters, and using the LES technique, a good agreement with the experimental data could be obtained. The equipment of the Computer Graphics Laboratory is important for the visualization of both the initial setup of the calculations and of the results obtained.
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