[gmx-users] how to use GROMACS to model carbon nanotubes

Wed Apr 23 03:06:15 CEST 2008

I have put together this general response to the vast amounts of e-mails I
have been receiving as of late in regards to how to use GROMACS to model
carbon nanotubes.

################ New GROMACS Users ################

First if you are new to GROMACS step on before you even install the program
is to read the manual! It is not that long and it will keep you from making
your self look stupid by asking questions that are very clearly covered in
it.

Second run the tutorials and make sure that your installation is functioning
properly.

Third make sure that all your files are UNIX formatted while this can cause
major problems otherwise.

Fourth become familiar with the formatting of a *.pdb file and what exactly
a residue is!

################ New to Simulations Containing CNT's ################

Now once you have done all of this you are ready to start learning how to
use GROMACS for your CNT simulations.

First I would start with using my site to get a general idea of what a basic
run through for a CNT simulation entails:

 <http://cs86.com/CNSE/SWNT.htm> http://cs86.com/CNSE/SWNT.htm

!!!!!!!!! Please note that this has not been updated for changes in the most
current version.

For *.pdb files you might want to use an application called Nanotube
Modeler, it can be found at  <http://www.jcrystal.com/products/wincnt/>
http://www.jcrystal.com/products/wincnt/

It allows for larger nanotubes then the method I have on the site and even
offers the ability to use capped tubes. I have worked with the developer to
make it so that the output *.pdb files have correct bond records although
note that some modification must be made to the files (commenting out the
first I believe 2 lines or so, and naming your residues properly. This can
be looked up easily and you should know how since you know what a residue is
by now and where they are in your *.pdb file). The application does cost
money but the time you save not hand coding is invaluable.

################ When You Start Having Problems ################

So when you start having problems which will probably be early and often if
you are anything like me!

First consult the Gromacs wiki it can be found at:
<http://wiki.gromacs.org/index.php/Main_Page>
http://wiki.gromacs.org/index.php/Main_Page 

Next search the mailing list to see if your problem has already been solved,
more then likely it has, and you can do that at the following:

 <http://www.gromacs.org/component/option,com_wrapper/Itemid,165/>
http://www.gromacs.org/component/option,com_wrapper/Itemid,165/

!!!!!!!!!!!! Make sure you check the appropriate boxes for your search, i.e.
'Mailing Lists' This is how I figured out most of my problems and the ones I
asked are also documented, try searching things like 'cnt' and 'swcnt' or
even looking for threads involving me (Christopher Stiles) they would have
been from the summer months of 2007 mainly.

When all else fails ask your question clearly on the mailing list which can
be found:

<http://www.gromacs.org/index.php?option=com_content&task=view&id=73&Itemid=
76>
http://www.gromacs.org/index.php?option=com_content&task=view&id=73&Itemid=7
6 

!!!!! Please make sure you are very clear while it will save you and the
people nice enough to respond lots of time! So what I mean by being clear is
include any errors you are having as they appeared when you get them. Also
include all step you have made previously including the commands you used
and how you modified any files. 

Also VERY IMPORTANT, pose your questions on the mailing list and not
personally to individuals e-mail addresses. This way when this person is
nice enough to take time out of their day to answer your question, others
may benefit from the question and answer.

################ Analyzing Your Data ################

Since you have read the manual you know there are lots of great tools built
in! So use them! Although I did run into some problems getting them to do
exactly what I wanted to do so I utilized another application. For my
analysis of my data I use an application called VMD it can be found at the
following address:
<http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD>
http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

With this application I use Tcl/Tk scripts to analyze at the data. This
application is very useful in producing nice images for presentations as
well!

################################################################

At any rate that's the best I can do since I am graduating in May. Also
please note that this is just what I learned to do over the last year so I
am no expert by any means, and I am just trying to help others that wish to
attempt similar things. I thank all those that have helped me along the way!

Additionally if some one would like to put this on GROMACS's wiki please
feel free to do so, I would but with graduation coming up I don't even have
time to be writing this. If you would like the files I have on my site those
can be provided for this purpose as well!

Cheers!

~Christopher Stiles

College of Nanoscale Science and Engineering (CNSE) State University of New
York, Albany, New York 12203, USA

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