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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>################ New GROMACS Users ################<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>Second run the tutorials and make sure
that your installation is functioning properly.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>Third make sure that all your files are UNIX
formatted while this can cause major problems otherwise.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>Fourth become familiar with the formatting
of a *.pdb file and what exactly a residue is!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>################ New to Simulations
Containing CNT’s ################<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>Now once you have done all of this you are
ready to start learning how to use GROMACS for your CNT simulations.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>First I would start with using my site to
get a general idea of what a basic run through for a CNT simulation entails:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><a href="http://cs86.com/CNSE/SWNT.htm"><font
color=navy><span style='color:navy'>http://cs86.com/CNSE/SWNT.htm</span></font></a><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>!!!!!!!!! Please note that this has not
been updated for changes in the most current version.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'>For
*.pdb files you might want to use an application called Nanotube Modeler, it
can be found at <a href="http://www.jcrystal.com/products/wincnt/"><font
color=navy><span style='color:navy'>http://www.jcrystal.com/products/wincnt/</span></font></a><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>################ When You Start Having Problems
################<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>So when you start having problems which
will probably be early and often if you are anything like me!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>First consult the Gromacs wiki it can be
found at: <a href="http://wiki.gromacs.org/index.php/Main_Page"><font
color=navy><span style='color:navy'>http://wiki.gromacs.org/index.php/Main_Page</span></font></a>
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>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:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><a
href="http://www.gromacs.org/component/option,com_wrapper/Itemid,165/"><font
color=navy><span style='color:navy'>http://www.gromacs.org/component/option,com_wrapper/Itemid,165/</span></font></a><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>!!!!!!!!!!!! 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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>When all else fails ask your question
clearly on the mailing list which can be found:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><a
href="http://www.gromacs.org/index.php?option=com_content&task=view&id=73&Itemid=76"><font
color=navy><span style='color:navy'>http://www.gromacs.org/index.php?option=com_content&task=view&id=73&Itemid=76</span></font></a>
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>!!!!! 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. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>################ Analyzing Your Data ################<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'>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: <a
href="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"><font
color=navy><span style='color:navy'>http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD</span></font></a><o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'>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!<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'>################################################################<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'>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!<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'>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!<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'>Cheers!<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:11.0pt;font-family:Arial;color:navy'>~Christopher
Stiles<o:p></o:p></span></font></p>
<p class=MsoNormal><st1:PlaceType w:st="on"><font size=2 color=navy face=Arial><span
style='font-size:11.0pt;font-family:Arial;color:navy'>College</span></font></st1:PlaceType><font
size=2 color=navy face=Arial><span style='font-size:11.0pt;font-family:Arial;
color:navy'> of <st1:PlaceName w:st="on">Nanoscale</st1:PlaceName> Science and
Engineering (CNSE) <st1:PlaceType w:st="on">State</st1:PlaceType> <st1:PlaceType
w:st="on">University</st1:PlaceType> of <st1:State w:st="on">New York</st1:State>,
<st1:place w:st="on"><st1:City w:st="on">Albany</st1:City>, <st1:State w:st="on">New
York</st1:State> <st1:PostalCode w:st="on">12203</st1:PostalCode>, <st1:country-region
w:st="on">USA</st1:country-region></st1:place><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
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