A simple polymer simulation

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1

My data file contains 3 polymer molecules of polyethylene of 200 carbon atoms each. I am very new to lammps and I have tried to minimize the molecule and it is not showing any errors. The only problem is that the molecule is not getting minimized as seen through the dcd file, i.e., the polymer molecule just comes closer and vibrates from the same position through out.

It will be great if anyone can help me with this.

My configuration file :

units real
boundary p p p
atom_style full

read_data final.in

pair_style lj/cut/coul/cut 12.0
bond_style harmonic
angle_style harmonic
dihedral_style opls
pair_modify mix geometric tail yes
special_bonds lj/coul 0.0 0.0 0.5

pair_coeff 1 1 0.066 3.50 # CT
pair_coeff 2 2 0.03 2.50 # HC
bond_coeff 1 268.0 1.529 # CT-CT
bond_coeff 2 340.0 1.090 # CT-HC
angle_coeff 1 58.35 112.7 # CT-CT-CT
angle_coeff 2 37.5 110.7 # CT-CT-HC
angle_coeff 3 33.0 107.8 # HC-CT-HC
dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT
dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC
dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC

velocity all create 300.0 20
fix 1 all nve
run 100
minimize 1.0e-4 1.0e-6 100 1000
write_restart min.restart

timestep 1.0
reset_timestep 0
neigh_modify every 10 delay 20 check yes
thermo 400
thermo_style multi

velocity all scale 300.0

unfix 1
fix 1 all npt temp 300 300 100 aniso 0.0 0.0 1555
fix 2 all langevin 300.0 300.0 50.0 1233

dump 1 all dcd 400 18xmixedhexane-eq.dcd
dump_modify 1 unwrap yes
run 100000
unfix 1
unfix 2

compute eng all pe/atom
compute eatoms all reduce sum c_eng

reset_timestep 0
fix 1 all nvt temp 300.0 300.0 100.0
thermo 20
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms
min_style cg
minimize 0.0 0.0 500000 1000000

write_restart eq.restart
write_data final1.in

My data file :

LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.5 on Sat Dec 03 22:51:04 IST 2016
1806 atoms
1803 bonds
3600 angles
5373 dihedrals
0 impropers
2 atom types
2 bond types
3 angle types
3 dihedral types
0 improper types
-100.444485 100.150112 xlo xhi
-100.575669 100.180431 ylo yhi
-100.702575 100.205925 zlo zhi

Masses

1 12.011000 # CT
2 1.008000 # HC

Atoms

1 1 1 -0.180000 -56.376385 -0.182120 1.002175 # CT POL
2 1 1 -0.120000 -56.221386 0.276880 -0.463825 # CT POL
3 1 1 -0.120000 -55.416386 -0.709120 -1.335825 # CT POL
4 1 2 0.060000 -55.692383 1.246881 -0.532825 # HC POL
5 1 2 0.060000 -57.239384 0.429880 -0.882825 # HC POL
6 1 1 -0.120000 -53.930386 -0.692120 -0.929825 # CT POL
7 1 2 0.060000 -55.481384 -0.347120 -2.384825 # HC POL
8 1 2 0.060000 -55.844383 -1.733119 -1.289825 # HC POL
9 1 1 -0.120000 -53.011383 -1.485120 -1.866825 # CT POL
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Also it will be great if you can tell me from where I can learn about md simulation for polymers in lammps.

2

My data file contains 3 polymer molecules of polyethylene of 200 carbon
atoms each. I am very new to lammps and I have tried to minimize the
molecule and it is not showing any errors. The only problem is that the
molecule is not getting minimized as seen through the dcd file, i.e., the
polymer molecule just comes closer and vibrates from the same position
through out.

please understand that it is not the purpose of this mailing list to
verify and correct anybody's input or to provide tutorials and
training on fundamental MD techniques or explain your input to you.

It will be great if anyone can help me with this.

you should ask your adviser/supervisor or your colleagues or
collaborators for help.

[...]

Also it will be great if you can tell me from where I can learn about md
simulation for polymers in lammps.

again, this is something you should discuss with your
adviser/supervisor as this is his/her responsibility to make certain
that you are sufficiently trained and prepared for the tasks that get
assigned to you. please note, that learning about MD in general and MD
for polymers has very little to do with LAMMPS itself and the
understanding of simulating these kind of systems are independent of
the MD software used.

axel.

3

Hi,

I can see that there are some basic mistakes in your input file.
You have used fix nve before minimization (minimization should be the first thing before any running). Then, later you used fix npt together with fix langevin, which does not make sense (two thermostat together?!).

If you are a beginner, you can try some lammps example, in the example folder.
You can then extend those example files more precisely based on your need and knowledge.