[gmx-users] g_bundle

David spoel at xray.bmc.uu.se
Thu Jul 10 08:43:00 CEST 2003

On Thu, 2003-07-10 at 06:30, Senthil Kandasamy wrote:
> Just thinking out loud and wanted to make sure I was interpreting this
> correctly. I am interested in finding the angle, an alpha helix forms
> with respect to the membrane normal (Z-axis )in  a membrane simulation.
> So, I used g_bundle with the -z option and set "-na 1". I specified the
> two groups to be the C-alpha of the first and the last amino acids.
> Then, bun_tilt.xvg should show the approximate angle that the helix
> forms with the z axis. I think I am correct...Just need some
> corroboration as a confidence booster...
> Thanks.
Use the source, Senthil....

If in doubt check the source code. I think your interpretation is
consistent with the help text, but I haven't written the program...

> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list