CHM 579 Assignment #5

Molecular Simulations - Molecular Dynamics of heterogenious systems


Due on Monday, March 27, 2020 at 11:59 PM

Overview:

The Assignment:

Part 1 - Molecular Dynamics with NAMD & VMD

This part of the assignment deals with running simulations and understanding how to analyze output from Molecular Dynamics (MD) simulations. The output of a MD program is a series of time-resolved coordinates for all of the atoms in the simulation. The code widely used in the MD community is GROMACS. It is one of the fastest MD software out there. Due to the complexity of using the code (only for Linux and MacOS and assumes Linux/Unix background), it would not be fair for all students to run simulations with it. Thus, we have decided to use NAMD, a MD simulation program developed by Theoretical and Computational Biophysics Group at UIUC in conjunction with VMD, the molecular viewing program. VMD has the capability to work with NAMD in order to display the results of a simulation as they are calculated (Interactive MD). As new atomic coordinate timesteps are generated by the simulation process, they can be transferred directly over to VMD, which can then animate the molecule. A major new feature in VMD is the ability to add perturbative steering forces to a running simulation, which are incorporated directly into the dynamics calculation. You will run both Interactive MD and Steered MD for this assignment.

In order to complete this assignment, you will require to have up-to-date versions of the following software, properly installed on your computer, as mentioned on the NAMD tutorial website:

For windows users, a proper work path should be set for the installed softwares. Suppose these softwares are installed under the following directories:

The work path can be created in different ways. One can either append the following command in C:\autoexec.bat and execute it or type this command in a DOS prompt:

path=C:\Program Files\University of Illinois\VMD;C:\NAMD;

Part 1A: Deca-alanine in vacuum

To make things simple for you we have chosen a tutorial from the NAMD website which you can replicate with different parameters and actually run simulations on your computer. You would be simulating deca-alanine in vacuum. A biologically relevant simulation would involve water molecules but in this case one can get to know a lot about structural features in deca-alanine in vacuum as time progresses in the simulation.

The deca-alanine tutorial will get you started with NAMD. You can get the pdf file for the tutorial here. Please NOTE that only pages 1-11 are relevant in the tutorial, though you can read further to get an idea of TCL. A feature of NAMD is that we can use TCL scripting language for analysis and simulation. We do not expect you to do any programming in TCL for the purpose of this assignment. Thus, we would be providing all the files needed to start the simulation. You should use VMD Extension for analysis as mentioned in the VMD tutorial on the VMD website. Please feel free to look for any good tutorials for VMD analysis for MD online, but ALWAYS reference it. We would try to update the VMD tutorial as well, to help with this assignment. You would only need to change the parameters for different simulations as asked below:

  1. Download and install the latest version of VMD and NAMD on your computer. Download the tar-zipped set-up files to get you started with the simulation. Please make sure that the current directory contains all the files downloaded. For windows users, create a folder files and download all the set-up files in this directory. At the command prompt make files as the current directory.

  2. The Interactive MD is for you to see how does the deca-alanine behaves with simulation. Follow the instructions in the tutorial for Interactive MD:

  3. Run Steered Molecular Dynamics (SMD) for 500 ps on deca-alanine in vacuum at 300K, 400K and 450K by changing the parameters in the smd.namd file. Note this is not an interactive MD but you should analyze the MD trajectory using VMD. You will notice that the SMD uses smd.tcl file for the force it applies on the atoms in simulation as explained on page 9 of the tutorial. Feel free to change the force-constant (k) paramter in the smd.tcl file to make the simulation work for 500ps.

Part 2 - Molecular Dynamics set-up with Gromacs

This part of the assignment deals with running simulations and understanding how to set-up simple systems with Gromacs and understand the output from Molecular Dynamics (MD) simulations. For this part of the assignment, please follow the instructions in the PDF files given below and answer the questions asked in the files:

Part 2A: Molecular Dynamics of Solvated Acetone

Note that the file required to do this assignmnet is here.

Part 2B: Molecular Dynamics of Lysozyme in Water

NOTE:

Please feel free to email the instructor if you have any questions about this assignment. Start early!!!

Handing Things In:

  1. Please remember to properly cite scientific papers/web pages you used for your assignment! You can find the reference to VMD, NAMD and GROMACS on their website. It is required to cite these references if you are using VMD or NAMD in your assignment. Plagiarism will not be tolerated. It is OK to include some well-written quotes in your assignment, but your descriptions should be mostly in your own words, so we can evaluate your understanding of the material.

How You Will Be Graded

  1. You answer all the questions asked on this page as well as in the linked PDF files of tutorials and labs.
  2. It is important to show that you understand things and not merely say 'yes' or 'no' for answers to the questions and grading will be done on your reasons/explanations to things that are asked in this assignment.
  3. Feel free to include any movies and illustrations for all parts of the assignment. Like we have discussed - think of the assignment as a research online paper where you can include illustrations to elaborate the points you are making as part of your results and discussions.



Problems? Questions about the Page or the Class? Contact the instructor