Question:
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 A protein channel that we have discussed during the 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 ?-helical dimeric structure of the Gramicidin A channel. One way to address this question is to perform simulations both with and without including 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, also available for download on Blackboard under Assignments), 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).
1) As you can see, these files include VMD scripts (i.e., 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, list all the file names, and describe briefly but correctly their content and why are they needed for, using no more than 3 sentences for each file.
2) Discuss the steps that can be used to setup and run the Gramicidin A simulations mentioned at point (1) above (using less than 150 words). List and describe briefly all the simulation parameters included in the NAMD configuration files that you think that are important for characterizing these simulations (so that somebody reading your report could reproduce your results).
3) Using either the results of your own simulations (preferred, for maximum credit points) 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. State clearly what statistical physics quantities one needs to analyze in order to show that the minimization, heating and equilibration steps were performed properly. If you perform your own simulations, state how long are your trajectories (they should be at least as long as the trajectories included in the files Grama_mem.zip and Grama_wat.zip). Note that it is not absolutely necessary to run your own simulations in order to complete fully the steps of this final project, since sample trajectories are already included.
4) Using the dcd trajectory file included in Grama_mem.zip, visualize the results of the simulations with the membrane and describe the conformational dynamics of the lipid bilayer membrane. Write a formula for calculating the average distance between the P atoms in the two membrane leaflets, and discuss if this is a good approximation of the thickness of a cellular lipid membrane. Extract and plot on the same graph the average distance between the P atoms in the two membrane leaflets, and the average distance between nearby P atoms in one leaflet.
5) Using the dcd trajectory files included in Grama_mem.zip and Grama_wat.zip for the results of the simulations with and without the membrane, (i) describe in a few sentences the role played by the surrounding lipid bilayer membrane in the stability of the ?-helical dimeric structure of the Gramicidin A channel, and (ii) measure and plot a numerical quantity to illustrate the role of the membrane.
6) Using the same dcd files as above, extract, plot and analyze at least four structural descriptors (for example the RMSD value) that would reflect the main changes occurring in the Gramicidin A channel simulated with and without the membrane. State briefly (less than 50 words) which structural descriptors would be good reaction coordinates that could capture clearly the structural changes observed during these simulations, and explain why.
7) Describe the mechanism (pathway) characterizing the structural changes in Gramicidin A. State which amino acids seem to play an important role in this mechanism and in the stabilization of the channel structure, and explain why are they important? (less than 100 words),
8) Describe briefly the specific: (i) physical model used for water molecules, and the dynamics of water molecules used here (less than 100 words), and (ii) physical model used for the lipid molecules, and the dynamics of the lipid molecules used here (less than 100 words).
9) Using the same dcd files as above, calculate, plot and analyze the number of water molecules that are located inside the Gramicidin protein in each case. Describe (less than 100 words) the physical interactions that control the dynamics of water molecules while they are inside the protein.
10) Propose briefly (using max. 250 words total) five realistic, possible additional, future computational experiments that you could do using the same programs and approach to test or to extend your findings from this study.