Please make sure that VMD (https://www.ks.uiuc.edu/Research/vmd) is installed on your own computer. Download also the NAMD files (https://www.ks.uiuc.edu/Research/namd), and make sure that you can access the online or PDF versions of the VMD and NAMD user guides.
Note: You will find included below instructions for the specific final project on structural modeling of the Gramicidin Aprotein channel that we have discussed during the last lectures. As we have discussed in the class, for this final project, we could use VMD and NAMD to study how important is the effect of the surrounding lipid bilayer membrane on the stability of the β-helical dimeric structure of the Gramicidin A channel. One trivial way to address this question is to perform simulations with and without the lipid membrane.
You can download examples of setup and configuration files for these simulations from https://sites.google.com/site/buchete/Grama_mem.zip (for a system including the membrane), and from?https://sites.google.com/site/buchete/Grama_wat.zip (for a system including only the protein and water molecules, without the lipid membrane).
Question) As you can see, these files include VMD scripts (that show you how to setup your systems automatically), configuration files for NAMD (needed to perform the actual simulations), as well as the results of some relatively short simulations of these systems (NPT runs of about 2 ns, saved every 20 ps). Download these files and describe briefly but correctly their content and why are they needed, using no more than three sentences for each file.
Question) Discuss the steps that can be used to setup and run the Gramicidin A simulations mentioned at point (1). List and describe briefly all the simulation parameters included in the configuration files that you believe that are crucial in characterizing these simulations (so that somebody reading your report could reproduce your results).
Question) Using either the results of your own simulations (preferred) or just the output files for the trajectories included in the files Grama_mem.zip and Grama_wat.zip, extract and plot the data needed to show that the minimization, heating and equilibration steps were performed properly.
Question) Using the dcd files included in Grama_mem.zip and Grama_wat.zip, visualize the results of the simulations with and without the membrane and describe the role played by the surrounding lipid bilayer membrane in the stability of the β-helical dimeric structure of the Gramicidin A channel.
Question)Using the same dcd files as above, extract, plot and analyze at least three structural descriptors (for example RMSD, radius of gyration, end-to-end distance, or other measures such as distances or angles) that would reflect the main changes occurring in Gramicidin A channel simulated with and without the membrane. Which structural descriptors would be good reaction coordinates that describe the structural changes observed during these simulations?
Question)Describe the mechanism (pathway) characterizing the structural changes in Gramicidin A. Which amino acids seem to play an important role in this mechanism and in the stabilization of the channel structure?
Question)Propose briefly possible future simulations and/or experiments that may be used to test or to extend your findings from this study.