[gmx-users] mass center of each molecule

Justin Lemkul jalemkul at vt.edu
Wed Jul 25 13:13:36 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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