Molecular Dynamics Simulations GLA

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by Benjamin Drexler and Fabian Grandke

Introduction

The aim of the task was to simulate the molecular dynamics of our protein. For that we used the tool GROMACS that has been used in the previous task, as well. Molecular dynamics are very useful to visualize the atomic movements within a protein. In our case we want to investigate, if there are differences between the molecular dynamics of the wildtype of the protein and the two mutations I117S and Q283P.

Methods

According to the task description we had to prepare some files and did a lot preprocessing steps, before we submit our final calculation to the LRZ.

Preparation

At first we had to prepare our files. Thereto we completed missing sidechains and removed hydrogen atoms.

GROMACS files

In this step we created a box around the protein and filled it with water. Then we added the particular Na and Cl ions, made sure that the charge is neutral ,and that there are no clashes between the initial crystal water and the box-fill-water.

Minimization

In this step first the solvent was minimized and then the solvent and the side chains of the protein were minimized in combination.

Equilibration of the system

The equilibration process consists of two steps of heating up the system. First the particle number and volume have been kept constant, while the pressure changed. Secondly the particle number and pressure were kept constant, while the volume changed. In both steps the temperature was increased during many single steps.

Production run

The heated system then got finished for the final molecular dynamics simulation.

LRZ

The previous prepared files were submitted to the LRZ Cluster and are calculated there, due to the fact that huge calculation powers are required.

Results/Discussion

The results of the molecular dynamics simulation can be found here.

References

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