[gmx-users] How to measure distance between two COM (centre of mass) of two group of atom

[Md. Imrul Reza Shishir]

Dear all
How do I measure distance between two COM (centre of mass) of two group of
atom. I want to measure the strain of my simulation system.
​[image: Inline image 3]​
​For that purpose i want to apply following ​analysis to the initial
structure and final structure to measure the distance.
​
"gmx distance -s *.tpr -f *.gro -n index.ndx -oall *.xvg​"

​Is this process is correct? What else should be the right procedure. I am
little bit confused with the output xvg file result. From where how can I
measure the distance.​

-- 
*Md Imrul Reza Shishir*
Master Student
*Inha University*