On 7/25/12 7:06 AM, akn wrote:
Dear gmx users,
I want to calculate the center of mass of each molecule in the system all
through the simulation time.
When I used "g_traj -f traj.xtc -s topol.tpr -n index.ndx -ox coord.xvg
-com'' command, I obtained the center of mass of the system
I tried some ways to get the mass center of each molecule but I was not able
to successful find it.
Similarly I need the inertia axis of each molecule all through the
simulation time but again I found
the average values at each step.
Could you please tell me how I can easily do these calculations by Gromacs
utility?
You need index groups that specify each molecule individually and you can use a
shell script to loop through all of the desired groups. I posted such a script
to the list just a few days ago when a similar question arose.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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