Ask Question, Ask an Expert

+1-415-315-9853

info@mywordsolution.com

Ask Programming Language Expert

Please make sure that VMD (http://www.ks.uiuc.edu/Research/vmd) is installed on your own computer. Download also the NAMD files (http://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 problem is to perform simulations with and without the lipid membrane.

You can download exs of setup and configuration files for these simulations from http://sites.google.com/site/buchete/Grama_mem.zip (for a system including the membrane), and from?http://sites.google.com/site/buchete/Grama_wat.zip (for a system including only the protein and water molecules, without the lipid membrane).

problem) 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.

problem) 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).

problem) 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.

problem) 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.

problem)Using the same dcd files as above, extract, plot and analyze at least three structural descriptors (for ex 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?

problem)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?

problem)Propose briefly possible future simulations and/or experiments that may be used to test or to extend your findings from this study.

Programming Language, Programming

  • Category:- Programming Language
  • Reference No.:- M9276

Have any Question? 


Related Questions in Programming Language

Assignmenta near expert at introductory problem solving and

Assignment A near expert at introductory problem solving and programming, you've decided to put your skills to good use by volunteering at SecurityCon, a security conference for IT professionals. The conference has space ...

James wants to buy a motorcycleinstructions the following

James wants to buy a motorcycle Instructions: The following programming problem can be solved by a program that performs three basic tasks-Input Data, Process Data, and Output Results. Use RAPTOR to design a suitable pro ...

Frans virtual fruit standuse the concepts and scenario from

Frans Virtual Fruit Stand Use the concepts and scenario from Assignment to help Fran's Virtual Fruit Stand increase the functionality of its online shopping cart. When a customer checks out, the shopping cart must store ...

Generate code for the following three-address statements

Generate code for the following three-address statements assuming a and b are arrays whose elements are 4-byte values. a) The four-statement sequence x = a[i] y = b[j] a[i] = y b[j] = x b) The three-statement sequence x ...

Programming assignmentdescription your algorithm first

Programming Assignment Description: Your algorithm first takes an input size (N) from the user and generates a random sequence of N integers ranging from -99999 to 99999. If N is less than 50, your program must print the ...

First write a program that reads students names followed by

First... Write a program that reads students' names followed by their test scores. The program should output each student's name followed by the test scores and the relevant grade. It should also find and print the highe ...

Pennies for pay you are hired for a job and your employer

Pennies for Pay You are hired for a job and your employer agrees to pay you each day. Your pay rate will be one penny the first day and two pennies the second day, four pennies the third day and continuing to double each ...

Programming languages assignment write the following as

Programming Languages Assignment Write the following as Prolog rules:  1. Implement a rule "dogEnthusiast". Someone is a "dogEnthusiast" if they own AT LEAST TWO dogs. Assume that the only types of facts available are: " ...

Creating methodssince you have created the data objects for

Creating Methods Since you have created the data objects for Harbor View Mooring, you now need to create processes associated with each object. In order to keep with good object-oriented practices of implementation hidin ...

Write a program that prompts the user to enter length and

Write a program that prompts the user to enter length and width dimensions for each room in a proposed house so that total floor space can be calculated for the entire house. After each length/width entry, ask the user i ...

  • 4,153,160 Questions Asked
  • 13,132 Experts
  • 2,558,936 Questions Answered

Ask Experts for help!!

Looking for Assignment Help?

Start excelling in your Courses, Get help with Assignment

Write us your full requirement for evaluation and you will receive response within 20 minutes turnaround time.

Ask Now Help with Problems, Get a Best Answer

WalMart Identification of theory and critical discussion

Drawing on the prescribed text and/or relevant academic literature, produce a paper which discusses the nature of group

Section onea in an atwood machine suppose two objects of

SECTION ONE (a) In an Atwood Machine, suppose two objects of unequal mass are hung vertically over a frictionless

Part 1you work in hr for a company that operates a factory

Part 1: You work in HR for a company that operates a factory manufacturing fiberglass. There are several hundred empl

Details on advanced accounting paperthis paper is intended

DETAILS ON ADVANCED ACCOUNTING PAPER This paper is intended for students to apply the theoretical knowledge around ac

Create a provider database and related reports and queries

Create a provider database and related reports and queries to capture contact information for potential PC component pro