# question on MSD calculation

Dear LAMMPS users,

I am using the following method to calculate MSD vs time at 600K. I am running FCC nickel structure with 1 Hydrogen(H) randomly placed using EAM potential. I have equilibrated my structure using energy minimization.When I run with 1 atom of hydrogen i get 0 MSD for hydrogen, but when I run with 2 atoms hydrogen I get MSD values. Can you please tell me why cannot I calculate for 1 atom of Hydrogen?

#equilibration
velocity all create 600 12345 mom yes rot no
fix 1 all npt temp 600 600 1 iso 0 0 1 drag 1

# Set thermo output

timestep 0.001
thermo 10000
thermo_style custom step lx ly lz press pxx pyy pzz pe temp
run 5000000

unfix 1

reset_timestep 0
fix 1 all nve
timestep 0.001

# Set thermo output

thermo 10000
compute 3 Hydrogen msd com yes
compute 4 Ni msd
thermo_style custom step temp pe press vol etotal

fix 3 he ave/time 10 5 1000 c_3[1] c_3[2] c_3[3] c_3[4] c_4[4] file 600.txt

compute 1 all temp
fix 2 all ave/time 10 5 1000 c_1 file temp6.profile
dump 2 all custom 100 600.dump id type xs ys zs

dump_modify 2 every 100000
compute 21 all pressure 1

fix 5 all ave/time 10 5 1000 c_21 file pressure6.profile
run 1000000
unfix 1
unfix 3
unfix 2
unfix 5
undump 2

Dear LAMMPS users,

I am using the following method to calculate MSD vs time at 600K. I am
running FCC nickel structure with 1 Hydrogen(H) randomly placed using EAM
potential. I have equilibrated my structure using energy minimization.When I
run with 1 atom of hydrogen i get 0 MSD for hydrogen, but when I run with 2
atoms hydrogen I get MSD values. Can you please tell me why cannot I
calculate for 1 atom of Hydrogen?

you can, but you are not doing it right.
what happens to the motion of one atom, if you subtract out the center
of mass from a group of atoms that contains just this one atom?