Benzene fix rigid

Dear lammps users,

I am trying to simulate Benzene molecule (only one).

I know that I can use ‘fix shake’ command for molecule within 4 atoms.

So, I am trying to use ‘fix rigid’ command to fix atoms of benzene.

But, I cant hold benzene ( it moves differently, not together).

Any suggesiton ?

Thanks,

Units

units real

Resion

boundary p p p

Force type

atom_style full

pair_style lj/cut/coul/cut 9 12

bond_style harmonic

angle_style harmonic

dihedral_style harmonic

improper_style cvff

Atom definition

read_data data_1Benzene.txt

velocity all create 298.15 8343 dist gaussian units box

Neighbor list

neighbor 2.0 bin

neigh_modify every 10 delay 0 check yes

Calculation

thermo_style custom step pe ke etotal temp press vol density

thermo 10

Minimization

minimize 1.0e-5 1.0e-7 1000 100000

Timestep

timestep 1

Fix molecular

group Benzene type 1 2

fix 1 Benzene rigid molecule

Dynamic type

fix 2 all npt temp 298.15 298.15 100 iso 1 1 100

Variable

variable fs equal 1*step

variable density equal “density”

variable vol equal “vol”

Print density

fix 3 all print 10 “{fs} {density}” file fsDensity.txt screen no

fix 4 all print 10 “{fs} {vol}” file fsVol.txt screen no

Dump

dump 1 all xyz 10 dump.xyz

dump_modify 1 element C H

Start running

run 10000

Save the restart file

write_restart restart1Benzene.txt

You cannot minimize rigid objects with minimize. It will not respect the constraints and the atoms can freely move away from each other. If you need to minimize, you can use bond and angle potentials to keep them in place.

You cannot minimize rigid objects with minimize. It will not respect the
constraints and the atoms can freely move away from each other. If you need
to minimize, you can use bond and angle potentials to keep them in place.

​or do simulated annealing.

axel.​