Simulation of C atoms in LAMMPS

Problem

• In this section we will try to simulate 500 atoms of carbon, in periodic(x,y,z) cubic box of dimentions 606060.Using LAMMPS code

Disclaimer:

• Please dont rely on the accuracy of data generated here in this sections, these examples are here only for a basic understanding of lammps.

Avogadro

• first open Avogadro GUI based softwere and then select Caron atom place any were in your work environment.

• Now go to Files > Export > Molecule

• And select save as type Gaussian Z-matrix input
• Now we have single atom in Z matrix format and it will look like this

• Now save this as .zmat format as required by fftool

• Now we will make c.ff file that contain about mass charge and force field parameters about atoms

• Now we will use these two file as input for fftool and we will create lammps data file
• type the following code

python3 fftool 500 c.zmat -b 60

FFtool for lammps data file

• At this point you have lammps data file (Please do proper research to find LJ parameters for C atom)
• Now we will lammps script for the simulation

clear
units 		real
boundary 	p p p

atom_style 	full

pair_style 	lj/cut 12.0

read_data 	data.lmp
#read_restart	restart.nve.2000100

pair_coeff    	1    1  0.065583     3.400000  # C C

minimize 	1.0e-4 1.0e-6 100 1000

neighbor 	2.0 bin
neigh_modify 	delay 0 every 1 check yes

timestep 	1.0

thermo_style	custom step time etotal ke pe evdwl temp press vol density 
thermo		10000

dump 		dcd all dcd 1000 C_500.dcd
dump_modify	dcd unwrap yes 

velocity        all create 298.15 90066 dist gaussian

fix 		mynve all nve
run		2000000
unfix		mynve
write_restart   restart.nve.*

fix             mynvt all nvt temp 298.15 298.15 100.0 
run             2000000
unfix           mynvt
write_restart   restart.npt.*

fix             mynpt all npt temp 298.15 298.15 100.0 iso 1.0 1.0 1000
run             10000000
unfix           mynpt
write_restart   restart.npt.*

• Above given script will run the simulation for total of 14 nanosecond
• 2 ns in NVE, 2ns in NVT and 10ns in NPT

Visualisation in VMD softwere

• After the simulation is over you will get .dcd file (snapshot of coordinates)
• Open VMD and go to Externsion > TkConsole and type the following

topo readlammpsdata data.lmp

pbc box

• After that select the molecule and go to File > Load Data into Molecule after all frames are loaded then again in console type

  pbc wrap -all