Analysis of the MD simulation trajectory

 

Both parts are independent from one another. Make sure to close VMD once you are done with one part, and open a new VMD session once you start the second part.

Part 1:

Load the trajectory file of 1UBQ equilibration in VMD.

Analyze the dynamical behavior of your protein along the simulation time.

– Calculate distances between residues to show the changes during the simulation time between:
o the CA atoms of Thr9 and Ile36;
o the NZ atom of Lys6 and CD of Glu64

– Calculate the dihedral angles Phi and Psi of residue 15.
– Calculate the RMSD along the trajectory time.
– Calculate the contact map of the protein and describe your results

Sample Solution

many novels during the 17th and 18th centuries, the main focus mirrored the ideas of The Enlightenment movement. In this review of sociologist Robert Wuthnow’s novel, author Philip Hoffman discusses the importance of literary standards during the Enlightenment. In the review, Hook analyzes how some uncommon works can come off as too discordant and irregular to procure positive feedback, while some other works can seem too practical and realistic and therefore won’t receive any praise and won’t attain any noteworthiness. Since Robert Wuthnow is the Professor of Sociology at Princeton University he serves as an extremely dependable source for my topic because of his education in the sociology field and being a highly distinguished author. Similar to how Hook analyzes the effect of unorthodox literary works, Voltaire strays away from the accepted standards of the time and explains the harsh realities of a rigid class structure during the Enlightenment in his novel. This review of Robert Wuthnow’s novel has provided me an immense amount of useful information on the cultural changes in society during this time period, as well as the effects these developmental shifts have on the social structure.

Hook, Sidney. “The Enlightenment and Marxism.” Journal of the History of Ideas, vol. 29, no.
1, 1968, pp. 93–108. JSTOR, www.jstor.org/stable/2708467

During The Enlightenment, there was a rigid class structure, dividing each person into one of the three classes: Upper Class, Middle Class, and the Working Class. Throughout this journal article, author Sidney Hook discusses the complex and unkempt relationship between Marxism and The The Enlightenment. In the article Hook analyzes the beliefs associated with The Enlightenment, faith in reason or science and the belief in the natural rights of man, and the reasoning behind the Marxist movements during that century, to regard socialism as a means of furthering democracy and to regard democracy simply as a means of furthering socialism. Unlike various other writers who boasted about their immense understanding of the theory of Marxism, Sidney Hook was the only experienced philosopher who was educated on the subject and was able to bring a detailed comprehension of Marx’s theory. This allowed him to provide readers with genuine sources in order to solve disputes and claims that became so visible during his life. By having the information given in this journal I will be able to distinguish the similarities between Marxist and Enlightenment thinkers and will have greater insights as to how the theory of Marxism affected the strict class structure during this time period.

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