hi
I want to calulate the diffusion( MSD ) of H2O in my polymer .I wrote the below input file but did not get the msd in the output file. what should I write to see the msd in the output file . thanks a lot
Best wishes
Ramin
LTA
units real
atom_style full
pair_style lj/cut 2.5
bond_style harmonic
angle_style harmonic
dihedral_style opls
read_data zeolite.lammps05
neighbor 2.0 bin
neigh_modify every 1 delay 1 check yes
timestep 0.001
thermo_style multi
#thermo 50
fix 3 all nvt temp 435.0 435.0 0.01
compute 1 all msd
dump 1 all custom 1 vmdoutput.lammpstrj id x y z vx vy vz
run 1000