Sorry that I get your time by my question . I am a new user of lammps and need help. I want to calculate the diffusion of water in zeolites ( LTA ) polymer I wrote this input file for my calculation . If it is possible for you to guide me that is it correct or not ?. I attached my data file .
thanks of your help

best wishes

Phd student of Istanbul technical university


units real
atom_style full
pair_style lj/cut 2.5
bond_style harmonic
angle_style harmonic
dihedral_style opls

read_data zeolite.lammps05
group water molecule 5 7
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 300.0 300.0 0.01
compute msd water msd com yes

fix msd water ave/time 1 1 1 c_msd[4] file msddumpfile

dump 1 all custom 1 vmdoutput.lammpstrj id x y z

run 1000

I don't know. I suggest you try it and see what happens.
I don't debug other people's input scripts. Rather I answer
specific questions about LAMMPS.