[gmx-users] Query about g_mindist

[soumadwip ghosh]

Hi all,
        I have a query about computing the number of native contacts formed
between a carbon nanotube and a RNA by g_mindist utility with the -d
option. The command I tried was g_mindist -f md.xtc -s md.tpr -od dist.xvg
-on numcount.xvg -d 0.5 and when prompted I selected CNT and DNA as two
groups. From the numcount.xvg files I plotted the graph. It looks the
following

https://drive.google.com/file/d/0B7SBnQ5YXQSLVVQwcVc2cWpJRnM/view?usp=sharing

My question is why the numbers in column Y such huge (say ~ 3000) while the
total number of atoms in CNT is 1500 and that in RNA is 500? Is it
calculating multiple contacts between one atom from CNT and whichever atoms
of RNA in between 5 Angstrom or something else is happening here. I am sure
that I selected CNT and RNA groups respectively when asked by the command
prompt. Any insight in this regard will be helpful.

Regards,
Soumadwip Ghosh
Senior Research Scholar
IITB
India