[gmx-users] g_mindsit contact analysis

[soumadwip ghosh]

Hi all,

I have simulated a duplex RNA in presence of a CNT in aqueous medium. The
gromacs version I used was 4.5.6. The two species were kept 2 nm apart to
begin with. I wanted to calculate how many RNA atoms were within 4 angstrom
distance from the CNT on a per-frame trajectory basis. I used the following
command:
 g_mindist -f md.xtc -s md.tpr -d 0.4 -n index.ndx -on nc.xvg

The CNT is composed of 1500 atoms while the nucleic acid is 370. The
contacts I am getting as a function of time is ~2000. Why is the value so
large? I did not specify COM or any particular atom belonging to CNT in my
index file and when prompted I selected the entire CNT and RNA for
g_mindist analysis. Is the number large because it calculates all the
atomic contacts between the two structures and prints it in the .xvg file?
For example, at 100 ps if each carbon atom  is having at least two RNA
contacts then the total contacts will be 3000. Is it being calculated this
way or something else is going on?

Thank you for your answer in advance

Soumadwip Ghosh