Carbon Nanotube

New GROMACS Users

First if you are new to GROMACS step on before you even install the program is to read the GROMACS 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 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 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 files). The application does cost money but the time you save not hand coding is invaluable.

When You Start Having Problems

Search the mailing list to see if your problem has already been solved - more then likely it has! 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. Please make sure you are very clear - 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, follow the advice here on getting help.

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.

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!