Hello everyone,

I am simulating a system of polymer and salt (Litfsi salt ion) using GAFF. I started with a small system comprising 5 polymer chains and 2 salt ions. The simulation works fine with a single processor. However, I encounter the error (i.e., Bond atoms 255 279 missing on proc 802 at step 2693 ) as the simulation is running in parallel. The input script is given below;

Could you please take a look at the script and advise me if there is something wrong with that?

@@@input [email protected]@@

units real

atom_style full

dimension 3

boundary p p p

read_data Data-Lammps-Small.dat

bond_style harmonic

angle_style harmonic

pair_style lj/cut/coul/long 10.0 10.0 # 10.0

special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0

#pair_modify tail yes

pair_modify mix arithmetic

kspace_style ewald 1e-8

#kspace_modify gewald 3.0

###pair coeffs

pair_coeff 1 1 0.1094001 3.3996700 #c-c

pair_coeff 2 2 0.0610000 3.1181500 # F-F

pair_coeff 3 3 0.0157000 2.4713500 # H-H

pair_coeff 4 4 0.0183000 2.0259000 # LI-LI

pair_coeff 5 5 0.1700000 3.2500000 # N-N

pair_coeff 6 6 0.1700000 3.2500000 # N1-N1

pair_coeff 7 7 0.1700000 3.2500000 # N2-N2

pair_coeff 8 8 0.1700000 3.2500000 # N3-N3

pair_coeff 9 9 0.1700000 3.2500000 # N4-N4

pair_coeff 10 10 0.1700000 3.2500000 # N5-N5

pair_coeff 11 11 0.1700000 3.00001 # O-O

pair_coeff 12 12 0.2100000 2.9599200 # O1-O1

pair_coeff 13 13 0.2100000 2.9599200 # O2-O2

pair_coeff 14 14 0.2100000 2.9599200 # O3-O3

pair_coeff 15 15 0.2100000 2.9599200 # O4-O4

pair_coeff 16 16 0.2100000 2.9599200 # O5-O5

pair_coeff 17 17 0.2500000 3.5635900 # S-S

##bond coeffs

bond_coeff 1 299.99 1.5000 # C-C

bond_coeff 2 299.79 1.3497 # C-F

bond_coeff 3 299.99 1.111 # C-H

bond_coeff 4 299.9 1.430 # C-N1

bond_coeff 5 299.9 1.430 # C-N2

bond_coeff 6 299.9 1.430 # C-N3

bond_coeff 7 299.9 1.430 # C-N4

bond_coeff 8 299.9 1.430 # C-N5

bond_coeff 9 299.9 1.430 # C-O1

bond_coeff 10 299.9 1.430 # C-O2

bond_coeff 11 299.9 1.430 # C-O3

bond_coeff 12 299.9 1.430 # C-O4

bond_coeff 13 299.9 1.430 # C-O5

bond_coeff 14 299.60 1.8087 # C-S

bond_coeff 15 299.9 0.997 # H-N2

bond_coeff 16 299.9 0.997 # H-N3

bond_coeff 17 299.9 0.997 # H-N4

bond_coeff 18 299.9 0.997 # H-N5

bond_coeff 19 299.000 0.99000 # H-O5

bond_coeff 20 289.9 0.997 # Li-N

bond_coeff 21 284.20 1.6720 # N-S

bond_coeff 22 308.6 1.4533 # O-S

##angle coeffs

angle_coeff 1 50.30 119.70 # C-C-C

angle_coeff 2 50.30 119.70 # C-C-H

angle_coeff 3 71.29 126.01 # C-C-N1

angle_coeff 4 71.29 126.01 # C-C-N3

angle_coeff 5 71.29 126.01 # C-C-N4

angle_coeff 6 71.29 126.01 # C-C-N5

angle_coeff 7 36.183 110.10 # C-C-O1

angle_coeff 8 36.183 110.10 # C-C-O4

angle_coeff 9 36.183 110.10 # C-C-O5

angle_coeff 10 50.30 119.70 # C-N1-C

angle_coeff 11 70.76 118.18 # C-N2-C

angle_coeff 12 69.999 117.00 # C-N2-H

angle_coeff 13 70.76 118.18 # C-N3-C

angle_coeff 14 69.999 117.00 # C-N3-H

angle_coeff 15 70.76 118.18 # C-N4-C

angle_coeff 16 69.999 117.00 # C-N4-H

angle_coeff 17 70.76 118.18 # C-N5-C

angle_coeff 18 69.999 117.00 # C-N5-H

angle_coeff 19 50.30 120.0 # C-O4-C

angle_coeff 20 50.30 119.70 # C-O5-H

angle_coeff 21 30.64 100.0219 # C-S-N

angle_coeff 22 31.26 100.086 # C-S-O

angle_coeff 23 33.88 100.0736 # F-C-F

angle_coeff 24 30.16 100.096 # F-C-S

angle_coeff 25 37.81 118.92 # H-C-H

angle_coeff 26 47.33 118.36 # H-C-N3

angle_coeff 27 47.33 118.36 # H-C-N4

angle_coeff 28 28.67 109.00 # H-C-O4

angle_coeff 29 28.67 109.00 # H-C-O5

angle_coeff 30 50.30 119.70 # Li-N-S

angle_coeff 31 50.30 119.70 # N-S-O

angle_coeff 32 74.20 109.14 # N1-C-N2

angle_coeff 33 74.20 109.14 # N1-C-N5

angle_coeff 34 50.30 119.70 # N1-C-O1

angle_coeff 35 74.20 109.14 # N2-C-N3

angle_coeff 36 74.20 109.14 # N2-C-N5

angle_coeff 37 50.30 119.70 # N2-C-O2

angle_coeff 38 50.30 119.70 # N3-C-O2

angle_coeff 39 50.30 119.70 # N4-C-O3

angle_coeff 40 50.30 119.70 # N4-C-O4

angle_coeff 41 50.30 119.70 # O-S-O

angle_coeff 42 50.30 119.70 # O3-C-O4

angle_coeff 43 31.49 100.196 # S-N-S

##------------------------Minimization------------------------------

reset_timestep 0 ## reset timestep

thermo 100 ##

thermo_style custom step temp pe vol density press

minimize 1.0e-5 1.0e-7 1000 100000