LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
[lammps-users] Missing atoms OPLS force fied
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[lammps-users] Missing atoms OPLS force fied


From: DUNDAR YILMAZ <duy42@...122...>
Date: Thu, 24 May 2018 10:56:22 -0400 (EDT)

Hi,
I am trying to simulate polymer systems using OPLS force field.
The system consists of Polyethylene chains and peroxide molecules on top of them.
I build the structure PE and peroxide parts separately and merge them using read data command twice.
Everything works fine. I minimize the structure without any problem. The system is a slab, periodic in x-y directions only. I defined a LJ wall at top and bottom of the structure using :

fix bottomwall all wall/lj93 zlo 5.0 2 2 5
variable linear equal ramp(170,105.0)
fix topwall all wall/lj93  zhi v_linear 2 2 5
run 100000

The top wall moves down to 105A in 100000 steps to compress the system in order to set the correct density.To avoid close contacts I built the structure with low density at the beginning.
Still no problem here. Bottomwall is fixed.
I start data collection part, nvt simulation at 500K for 2000000 steps.
After 243398 steps I received this error: 

ERROR on proc 2: Dihedral atoms 17112 17117 17118 17032 missing on proc 2 at step 243398 (../ntopo_dihedral_al
l.cpp:72)

I searched this error, it says usually bad construction of structure like close contacts of atoms etc. However I do not think thats the case here because the simulation runs more than 300 000 steps before getting this error and also minimizes without any problem. Here is my neighbor settings:

neighbor        7.0 bin
neigh_modify    every 2 delay 2 check yes

I increased the skin size to see it helps but no luck. Increased the neighborlist build frequency but still error persists.
Finally my force field parameters:

pair_style lj/cut/coul/cut 10.0 8.0
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

#force field parameters
#

pair_coeff 1 1 0.066 3.5  # C sp3 carbon
pair_coeff 2 2 0.03 2.5   # H bonded to Carbon
pair_coeff 3 3 0.140 2.9  # Oxygen 


bond_coeff 1 268.0 1.529 # C- C bond
bond_coeff 2 340.0 1.09  # C-H bond
bond_coeff 3 320.0 1.41  # C-O bond
bond_coeff 4 400.0 0.96  # O-H bond
bond_coeff 5 525.0 1.48  # O-O bond

angle_coeff 1 58.35 112.7 # C-C-C
angle_coeff 2 37.50 110.7 # C-C-H
angle_coeff 3 33.00 107.8 # H-C-H
angle_coeff 4 80.00 118   # O-C-C
angle_coeff 5 80.00 118   # DUMMY
angle_coeff 6 80.00 118   # DUMMY
angle_coeff 7 80.00 118   # O-O-C

dihedral_coeff 1 0.527 -0.186 0.900 0.0 # C- C- C - C
dihedral_coeff 2 0.0  0.00 0.150 0.0 # C- C- C - H
dihedral_coeff 3 0.0  0.00 0.150 0.0 # H- C- C - H
dihedral_coeff 4 0.0  0.00 0.820 0.0 # O- C- C - C
dihedral_coeff 5 0.0  0.00 0.468 0.0 # O- C- C - H


I suspect my non bonded parameters but the density of the system is compatible with experiment which is a nice sign for correct vdW parameters. 
Is there anything that I am missing?
Thanks everyone.
Dundar Yilmaz