From: Claw Isthelaw (
Date: Sat Aug 11 2007 - 19:53:35 CDT

> Hi - I'm using VMD to plot bond distances and rmsd's from a trajectory,
> but I can't find a way to print or save the graph on a Mac (it says it
> can't use excel on macs). Can someone tell me what I'm missing or if it's
> just not possible? Thanks.

1) Instead of plotting the data in VMD, write the data to a file. The RMSDTT tool should have that option somewhere. Then use Excel to open the data file

2) Xmgrace is a good program. And if you have Darwin Ports installed, then just type 'sudo port install grace' in your terminal, but if not, then the build is pretty straight forward. Once you get that installed, VMD can plot directly to Grace and give you nice looking graphs. But if you are running VMD from Terminal, then you will need to open X11 before plotting, or else VMD will give you a "Failed Initializing GUI" error. I'm not sure if X11 comes preinstalled, but you can find it on your OSX install disc. Also, I'm not sure if the port install will give you some needed libraries (for saving pictures of your graphs and other things): libpng, libjpeg, fftw, netcdf. Darwin Ports will install all four of these using the same command 'sudo port install ' That's kind of alot of stuff you may have to go through, but Xmgrace is a really good program.

Jeff Tibbitt

Find a local pizza place, movie theater, and more….then map the best route!