[gmx-users] root-mean-square distance
dinadusti at yahoo.com
Sun Jan 29 08:09:17 CET 2012
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?
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users