Hi Mr.Baig Abdullah Al Muhit 

I think you use of under commands is enough and also maybe you diagram to output wrong..you should draw the third columns by the second column.

At last, Is your simulation just on graphene ?or other materials have been used? If so, you should change fix all to fix graphene.

compute        myRDF all rdf 1000 

fix 1 all ave/time 2500   2  2500 c_myRDF file tmp.rdf mode vector.

Hello Mahboubeh,

Thank you for replying. I plotted the figure with X-direction (2nd column) and Y-direction (3rd column) for C-C rdf. I created the data file for graphene from VMD. I only have carbon in graphene-not any other elements. As i understand from LAMMPS documentation, 2nd column of RDF output is the distance, and 3rd column is g(r). But still it is showing the first peak around 4 angstrom. What am I doing wrong?

Hello Andrea,

Thank you for replying. Here's an input file for water. The rdf for water is also wrong. It's 2.1 angstrom instead of 1 angstrom. That's why I am giving you this. I think I am doing something wrong in general:

units real

atom_style full

newton on

dimension 3

read_data wat.data

pair_style lj/cut/coul/long 10 10

bond_style harmonic

angle_style harmonic

dihedral_style none

improper_style none

pair_coeff 1 1 0.1553 3.5533

pair_coeff 2 2 0 0

pair_modify mix arithmetic tail no

bond_coeff 1 540.6336 1

angle_coeff 1 50 109.47

kspace_style pppm 1e-6

replicate 6 6 6

neighbor 3 bin

neigh_modify delay 0 every 1 one 10000 check yes

compute wattemp all temp

velocity all create 1 12345 temp wattemp dist gaussian mom yes rot no

compute poteng all pe/atom

compute watpot all reduce sum c_poteng

compute 5 all msd

compute myrdf all rdf 50 1 2

variable diff equal c_5[4]

variable mu equal c_meansq/(6*timestep)

variable pe equal c_watpot

min_style cg

minimize 1.0e-16 1.0e-16 100000 1000000

min_modify dmax 0.1

fix 1 all nve

fix 2 all langevin 1 1 100 1234

fix 7 all ave/time 2 50 100 c_myrdf[1] c_myrdf[2] c_myrdf[3] file COM.rdf mode vector

fix 8 all ave/time 2 50 100 c_5[4] file msd.rdf mode scalar

thermo 100

thermo_style custom step temp pe v_pe v_diff

run 10000

unfix 1

fix 3 all npt temp 1 1 100 iso 1 1 1000

dump 1 all xyz 100 wat.xyz

dump 3 all dcd 1000 hbond.dcd

run 10000

write_data wat2.data

 Hi Baig, 

I'm assuming you've already solved the problem. but if not, you should have converted R to sigma in lammps to match equations. So, instead of 3.5533 it should be around 3.1655. 

Good luck