[gmx-users] root-mean-square distance

dina dusti dinadusti at yahoo.com
Sun Jan 29 08:09:17 CET 2012

Dear Specialists,

I have a problem about computing of radius of micelle by root-mean-square-distance. Please help me.
I obtained radius of my micelle 2.4 nm by g_gyrate. 

g_gyrate -f md.xtc -s md.tpr -o gyrate.xvg -b 150000
I want compare it by rms distance. 

I use from g_rms as following:
g_rms -f md.xtc -s md.tpr -o distrmsd.xvg -n index.ndx -b 150000 
It result me 3.992290e+00 nm after averaging by g_analyze -f distrmsd.xvg -av
(the radius of a spherical micelle is defined as the rms distance of the headgroup atoms from the micelle center of mass, how should I define com of micelle in g_rms?)
I think I am wrong somewhere. 

May I ask you to help me,Please?

Best Regards
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120128/356822aa/attachment.html>

More information about the gromacs.org_gmx-users mailing list