Introductory Molecular Dynamics Simulations of Fullerenes - Revision history

Agarcia at 17:18, 7 July 2008

2008-07-07T17:18:19Z

← Older revision		Revision as of 17:18, 7 July 2008
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	Additional Problem		Additional Problem

	1. After comparing the above files and given the coordinates file for a nanocapsule, make a simulation of an nanocapsule. ~~(Hint: Copy and Paste files and make the appropriate changes)~~		1. After comparing the above files and given the coordinates file for a nanocapsule, make a simulation of an nanocapsule.
			(Hint: Copy and Paste files and make the appropriate changes)

	Further Exercises		Further Exercises

	1.Make a temperature dependent buckyball. Go to the open the script file for the bucky ball and activate the commands needed to simulate the bucky ball under a desired temperature. For this temperature dependent simulation a potential call Tersoff potential will be needed. Do the following step before running the simulation.		1.Make a temperature dependent buckyball. Go to the open the script file for the bucky ball and activate the commands needed
			to simulate the bucky ball under a desired temperature. For this temperature dependent simulation a potential call
			Tersoff potential will be needed. Do the following step before running the simulation.

	Further Step		Further Step

Agarcia at 17:15, 7 July 2008

2008-07-07T17:15:37Z

← Older revision		Revision as of 17:15, 7 July 2008
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	Why do we want to simulate fullerenes?		Why do we want to simulate fullerenes?

	Fullerenes are a group of molecules made with only carbon atoms. These molecules exhibit very special properties. The reason why scientists are interested in understanding the behavior of fullerenes is because they have extra ordinary properties in superconductivity, electricity and elasticity. They could have numerous applications to improve many of our existing products and develop new products. There are lots of unexplained answers regarding the behavior of fullerenes. Making simulations of these molecules is a safe and efficient approach.		Fullerenes are a group of molecules made with only carbon atoms. These molecules exhibit very special properties. The reason why scientists are interested in understanding the behavior of fullerenes is because they have extra ordinary properties in superconductivity, electricity and elasticity. They could have numerous applications to improve many of our existing products and develop new products. There are lots of unexplained answers regarding the behavior of fullerenes. Making simulations of these molecules is a safe and efficient approach and data can be used to be compared with experimental data.

	Procedure for simulating the bucky ball		Procedure for simulating the bucky ball
Line 9:		Line 9:
	Brainstorming:		Brainstorming:

	What would ~~you~~ ~~need~~ to make a simulation of a ~~buckyball~~?		What would be needed to make a simulation of a bucky ball?

	-The coordinates of each atom in space		-The coordinates of each atom in space
Line 21:		Line 21:
	Note: all the files needed for this activity are in a folder called etp07nanostructurefiles.		Note: all the files needed for this activity are in a folder called etp07nanostructurefiles.

	Step 1		'''Step 1'''

	Obtain the coordinates of the bucky ball. They are located in a file called buckyball.xyz . Make sure that you keep this file in that format. Place the buckyball.xyz file in the runs directory. It is assumed that you have installed MD++ properly. From the desktop, go to the menu bar and click on places and open the home folder. Open the Codes folder. Open the MD++ folder. Open the runs folder. Make a new folder and call it buckyball. Copy the buckyball.xyz file into the runs folder.		Obtain the coordinates of the bucky ball. They are located in a file called buckyball.xyz . Make sure that you keep this file in that format. Place the buckyball.xyz file in the runs directory. It is assumed that you have installed MD++ properly. From the desktop, go to the menu bar and click on places and open the home folder. Open the Codes folder. Open the MD++ folder. Open the runs folder. Make a new folder and call it buckyball. Copy the buckyball.xyz file into the runs folder.

	Step 2		'''Step 2'''

	Obtain the octave execution file of the bucky ball. They are located in a file called readbuckyball.oct . Make sure that you keep this file in that format. Place the octave file in the runs directory. Again from the desktop, go to the menu bar and click on places and open the home folder. Open the Codes folder. Open the MD++ folder. Open the runs folder. Copy the readbuckyball.oct file into the runs folder.		Obtain the octave execution file of the bucky ball. They are located in a file called readbuckyball.oct . Make sure that you keep this file in that format. Place the octave file in the runs directory. Again from the desktop, go to the menu bar and click on places and open the home folder. Open the Codes folder. Open the MD++ folder. Open the runs folder. Copy the readbuckyball.oct file into the runs folder.

	Step 3		'''Step 3'''

	From the runs directory, run the octave file by typing:		From the runs directory, run the octave file by typing:
Line 37:		Line 37:
	This will create a cn file called buckyball.cn. Go back to the MD++ directory.		This will create a cn file called buckyball.cn. Go back to the MD++ directory.

	Step 4		'''Step 4'''

	Now copy the script file called buckyball.script. Go to the scripts directory. Make a directory and call it myscripts. Now copy the the file buckyball.script into the myscripts folder.		Now copy the script file called buckyball.script. Go to the scripts directory. Make a directory and call it myscripts. Now copy the the file buckyball.script into the myscripts folder.

	Step 5		'''Step 5'''

	Now open the terminal emulator ( the icon that has the $ sign). Go to the MD++ directory by typing:		Now open the terminal emulator ( the icon that has the $ sign). Go to the MD++ directory by typing:

Agarcia at 17:10, 7 July 2008

2008-07-07T17:10:14Z

← Older revision		Revision as of 17:10, 7 July 2008
Line 3:		Line 3:
	Why do we want to simulate fullerenes?		Why do we want to simulate fullerenes?

	Fullerenes are a group of molecules made with only carbon atoms. These molecules exhibit very special properties. The reason why scientists are interested in understanding the behavior of fullerenes is because they have extra ordinary properties in superconductivity, electricity and elasticity. They could have numerous applications to improve many of our existing products and develop new products. There are lots of unexplained answers regarding the behavior of fullerenes. ~~I believe that making~~ simulations of these molecules is ~~the most~~ safe and efficient approach.		Fullerenes are a group of molecules made with only carbon atoms. These molecules exhibit very special properties. The reason why scientists are interested in understanding the behavior of fullerenes is because they have extra ordinary properties in superconductivity, electricity and elasticity. They could have numerous applications to improve many of our existing products and develop new products. There are lots of unexplained answers regarding the behavior of fullerenes. Making simulations of these molecules is a safe and efficient approach.

	Procedure for simulating the bucky ball		Procedure for simulating the bucky ball

Agarcia at 23:39, 1 July 2008

2008-07-01T23:39:53Z

← Older revision		Revision as of 23:39, 1 July 2008
Line 14:		Line 14:
	-The program that will create the graphics		-The program that will create the graphics

	What do need to change the physical properties of the bucky ball like the temperature, velocity, pressure of the system, etc.?		What do you need to change the physical properties of the bucky ball like the temperature, velocity, pressure of the system, etc.?

	-Appropriate potential energy approximation		-Appropriate potential energy approximation
Line 66:		Line 66:
	Additional Problem		Additional Problem

	1. After comparing the above files and given the coordinates file for a nanocapsule, make a simulation of an nanocapsule. (Hint: Copy and Paste files and make the appropriate changes)		1. After comparing the above files and given the coordinates file for a nanocapsule, make a simulation of an nanocapsule. (Hint: Copy and Paste files and make the appropriate changes)

	Further Exercises		Further Exercises

	1.Make a temperature dependent ~~bucky ball~~. Go to the open the script file for the bucky ball and activate the commands needed to simulate the bucky ball under a desired temperature. For this temperature dependent simulation a potential call Tersoff potential will be needed. Do the following step before running the simulation.		1.Make a temperature dependent buckyball. Go to the open the script file for the bucky ball and activate the commands needed to simulate the bucky ball under a desired temperature. For this temperature dependent simulation a potential call Tersoff potential will be needed. Do the following step before running the simulation.

	Further Step		Further Step

	Open the terminal emulator. Go to the MD++ directory by typing:		Open the terminal emulator. Go to the MD++ directory by typing:

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	'''Acknowledgments'''		'''Acknowledgments'''

	Professor Dr. Wei Cai for hosting me as fellow		Professor Dr. Wei Cai for hosting me as fellow
	Keonwook Kang, Graduate Stduent in prof. Wei Cai group		Keonwook Kang, Graduate Stduent in prof. Wei Cai group
	Mechanical Engineering and Computation Department, Durand Hall, Stanford University		Mechanical Engineering and Computation Department, Durand Hall, Stanford University

	'''References'''		'''References'''

Agarcia at 23:34, 1 July 2008

2008-07-01T23:34:55Z

Show changes

Agarcia: New page: Simulating Carbon Nanostructures and Their Interactions Under Different Physical Conditions Why do we want to simulate fullerenes? Fullerenes are a group of molecules made with only car...

2008-07-01T23:25:44Z

New page: Simulating Carbon Nanostructures and Their Interactions Under Different Physical Conditions Why do we want to simulate fullerenes? Fullerenes are a group of molecules made with only car...

New page

Simulating Carbon Nanostructures and Their Interactions Under Different Physical Conditions

Why do we want to simulate fullerenes?

Fullerenes are a group of molecules made with only carbon atoms. These molecules exhibit very special properties. The reason why scientists are interested in understanding the behavior of fullerenes is because they have extra ordinary properties in superconductivity, electricity and elasticity. They could have numerous applications to improve many of our existing products and develop new products. There are lots of unexplained answers regarding the behavior of fullerenes. I believe that making simulations of these molecules is the most safe and efficient approach.

Procedure for simulating the bucky ball

Brainstorming:

What would you need to make a simulation of a bucky ball?
-The coordinates of each atom in space
-The program that will create the graphics

What do need to change the physical properties of the bucky ball like the temperature, velocity, pressure of the system, etc.?
-Appropriate potential energy approximation
-MD++ code

Note: all the files needed for this activity are in a folder called etp07nanostructurefiles.
'''
Step 1'''
Obtain the coordinates of the bucky ball. They are located in a file called buckyball.xyz . Make sure that you keep this file in that format. Place the buckyball.xyz file in the runs directory. It is assumed that you have installed MD++ properly. From the desktop, go to the menu bar and click on places and open the home folder. Open the Codes folder. Open the MD++ folder. Open the runs folder. Make a new folder and call it buckyball. Copy the buckyball.xyz file into the runs folder.

'''Step 2'''
Obtain the octave execution file of the bucky ball. They are located in a file called readbuckyball.oct . Make sure that you keep this file in that format. Place the octave file in the runs directory. Again from the desktop, go to the menu bar and click on places and open the home folder. Open the Codes folder. Open the MD++ folder. Open the runs folder. Copy the readbuckyball.oct file into the runs folder.
Step 3
From the runs directory, run the octave file by typing:

./readbuckyball.oct

This will create a cn file called buckyball.cn. Go back to the MD++ directory.
Step 4
Now copy the script file called buckyball.script. Go to the scripts directory. Make a directory and call it myscripts. Now copy the the file buckyball.script into the myscripts folder.
Step 5
Now open the terminal emulator ( the icon that has the $ sign). Go to the MD++ directory by typing:

cd Codes/MD++/

All simulations are run from MD++ directory. To run the simulation of the bucky ball type:

bin/md_gpp scripts/myscripts/buckyball.script

A new graphics window will pop-up with the simulation of a bucky ball in 3D!!! Here are a few exciting exercises to learn the process.
Exercises
1.Repeat the same process to simulate a nanotube.
2.Repeat the same process to simulate a graphene sheet.
Analysis Questions
1.Compare the coordinate files for the three molecules. Describe the differences and write them down for discussion.
2.Compare the octave files for the three molecules. Explain the differences and write them down for discussion.
3.Compare the script files for the three molecules. Explain the differences and write them down for discussion.
Additional Problem
1. After comparing the above files and given the coordinates file for a nanocapsule, make a simulation of an nanocapsule. (Hint: Copy and Paste files and make the appropriate changes)
Further Exercises
1.Make a temperature dependent bucky ball. Go to the open the script file for the bucky ball and activate the commands needed to simulate the bucky ball under a desired temperature. For this temperature dependent simulation a potential call Tersoff potential will be needed. Do the following step before running the simulation.
Further Step
Open the terminal emulator. Go to the MD++ directory by typing:

cd Codes/MD++

now type:

make tersoff build=R TCL=no

This will compile the Tersoff potential in the bin directory. Now that the script file for the bucky ball has been modified, type:

bin/tersoff_gpp scripts/myscripts/buckyball.script

This will pop-up a new graphics window with a temperature-dependent bucky ball simulation. The other simulations can also be made temperature dependent by copying and pasting the sections.

Acknowledgments

Professor Dr. Wei Cai for hosting me as fellow
Keonwook Kang, Graduate Stduent in prof. Wei Cai group
Chris Tucker
Haneesh
Mechanical Engineering and Computation Department, Durand Hall, Stanford University

References
1.MD++
source: http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/
2.Fullerenes
source: http://en.wikipedia.org/wiki/Fullerene
3.Fullerene Science Module
source: http://www.chemistry.wustl.edu/~edudev/Fullerene/fullerene.html
4.What are fullerenes?
source: http://www.nottingham.ac.uk/~ppzjld/what.htm
5.Carbon Cages: LBL Scientists Study Fullerenes
source: http://lbl.gov/Science-Articles/Archive/fullerenes.html