ERROR on proc 96: Bond atoms 4437 4440 missing on proc 96 at step 6764478 (src/ntopo_bond_all.cpp:59)

LAMMPS LAMMPS Beginners
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1

Dear LAMMPS developers and users,

I have an issue when running my simulation : ERROR on proc 96: Bond atoms 4437 4440 missing on proc 96 at step 6764478 (src/ntopo_bond_all.cpp:59), and I need to fix it,

For you information, I’ve done geometry optimization using ORCA, and for packing my system box I’ve used PACKMOL,

This is my input :

# LAMMPS Input for BI and PA molecules 

# --- 1. SETUP ---
units           real
dimension       3
boundary        p p p
atom_style      full

# --- 2. FORCE FIELD DEFINITION ---
# These styles MUST match OPLS-AA requirements
pair_style      hybrid lj/cut/coul/long 12.0 12.0
pair_modify     mix geometric tail yes 
bond_style      harmonic
angle_style     harmonic
dihedral_style  opls
improper_style  cvff            # LigParGen uses cvff or harmonic for impropers
kspace_style    pppm 1.0e-5

# --- 3. LOAD SYSTEM ---
read_data       data_new_1_6.lmp     # topology + Packmol coordinates

pair_coeff    1    1 lj/cut/coul/long     0.170000     3.250000  # N00 N00
pair_coeff    2    2 lj/cut/coul/long     0.000000     0.000000  # H01 H01
pair_coeff    3    3 lj/cut/coul/long     0.070000     3.550000  # C02 C02
pair_coeff    4    4 lj/cut/coul/long     0.170000     3.250000  # N03 N03
pair_coeff    5    5 lj/cut/coul/long     0.070000     3.550000  # C04 C04
pair_coeff    6    6 lj/cut/coul/long     0.080000     3.500000  # C05 C05
pair_coeff    7    7 lj/cut/coul/long     0.070000     3.550000  # C06 C06
pair_coeff    8    8 lj/cut/coul/long     0.070000     3.550000  # C07 C07
pair_coeff    9    9 lj/cut/coul/long     0.070000     3.550000  # C08 C08
pair_coeff   10   10 lj/cut/coul/long     0.070000     3.550000  # C09 C09
pair_coeff   11   11 lj/cut/coul/long     0.070000     3.550000  # C0A C0A
pair_coeff   12   12 lj/cut/coul/long     0.070000     3.550000  # C0B C0B
pair_coeff   13   13 lj/cut/coul/long     0.070000     3.550000  # C0C C0C
pair_coeff   14   14 lj/cut/coul/long     0.080000     3.500000  # C0D C0D
pair_coeff   15   15 lj/cut/coul/long     0.070000     3.550000  # C0E C0E
pair_coeff   16   16 lj/cut/coul/long     0.070000     3.550000  # C0F C0F
pair_coeff   17   17 lj/cut/coul/long     0.170000     3.250000  # N0G N0G
pair_coeff   18   18 lj/cut/coul/long     0.070000     3.550000  # C0H C0H
pair_coeff   19   19 lj/cut/coul/long     0.170000     3.250000  # N0I N0I
pair_coeff   20   20 lj/cut/coul/long     0.000000     0.000000  # H0J H0J
pair_coeff   21   21 lj/cut/coul/long     0.070000     3.550000  # C0K C0K
pair_coeff   22   22 lj/cut/coul/long     0.070000     3.550000  # C0M C0M
pair_coeff   23   23 lj/cut/coul/long     0.070000     3.550000  # C0N C0N
pair_coeff   24   24 lj/cut/coul/long     0.070000     3.550000  # C0O C0O
pair_coeff   25   25 lj/cut/coul/long     0.070000     3.550000  # C0P C0P
pair_coeff   26   26 lj/cut/coul/long     0.070000     3.550000  # C0Q C0Q
pair_coeff   27   27 lj/cut/coul/long     0.030000     2.420000  # H0R H0R
pair_coeff   28   28 lj/cut/coul/long     0.030000     2.420000  # H0S H0S
pair_coeff   29   29 lj/cut/coul/long     0.030000     2.420000  # H0T H0T
pair_coeff   30   30 lj/cut/coul/long     0.030000     2.420000  # H0U H0U
pair_coeff   31   31 lj/cut/coul/long     0.030000     2.420000  # H0V H0V
pair_coeff   32   32 lj/cut/coul/long     0.030000     2.420000  # H0W H0W
pair_coeff   33   33 lj/cut/coul/long     0.030000     2.420000  # H0X H0X
pair_coeff   34   34 lj/cut/coul/long     0.030000     2.420000  # H0Y H0Y
pair_coeff   35   35 lj/cut/coul/long     0.030000     2.420000  # H0Z H0Z
pair_coeff   36   36 lj/cut/coul/long     0.030000     2.420000  # H10 H10
pair_coeff   37   37 lj/cut/coul/long     0.030000     2.420000  # H11 H11
pair_coeff   38   38 lj/cut/coul/long     0.030000     2.420000  # H12 H12
pair_coeff   39   39 lj/cut/coul/long     0.200000     3.740000  # P00 P00
pair_coeff   40   40 lj/cut/coul/long     0.210000     2.960000  # O01 O01
pair_coeff   41   41 lj/cut/coul/long     0.170000     3.120000  # O02 O02
pair_coeff   42   42 lj/cut/coul/long     0.170000     3.120000  # O03 O03
pair_coeff   43   43 lj/cut/coul/long     0.170000     3.120000  # O04 O04
pair_coeff   44   44 lj/cut/coul/long     0.000000     0.000000  # H05 H05
pair_coeff   45   45 lj/cut/coul/long     0.000000     0.000000  # H06 H06
pair_coeff   46   46 lj/cut/coul/long     0.000000     0.000000  # H07 H07

# --- 4. OPLS SPECIFIC SETTINGS  ---
neighbor        2.0 bin
neigh_modify    delay 0 every 1 check yes
special_bonds   lj/coul 0.0 0.0 0.5   # 0% interaction for 1-2/1-3, 50% for 1-4

# --- 5. MINIMIZATION ---
thermo          100
minimize        1.0e-8 1.0e-10 2000 10000
reset_timestep  0

# --- 6. EQUILIBRATION  ---
timestep        1.0
velocity        all create 10.0 12345 dist gaussian
fix             1 all npt temp 10.0 373.15 100.0 iso 1.0 1.0 5000.0
run             2000000    # 2 ns
unfix           1
reset_timestep  0

# --- Output setup ---
thermo 1000
thermo_style custom step etotal ke pe evdwl ecoul elong temp press vol density

# --- Trajectory ---
dump            1 all custom 1000 mix_anneal_1_6.lammpstrj id mol type x y z
dump_modify     1 sort id

# --- NPT/NVT Ensemble ---
# P = 1 atm
# Tdamp = 100 fs, Pdamp = 1000 fs
fix             2 all nvt temp 373.15 373.15 100.0
run             5000000    # 5 ns
unfix           2

fix             3 all npt temp 373.15 473.15 100.0 iso 1.0 1.0 1000.0
run             2000000    # 2 ns
unfix           3 

fix             4 all nvt temp 473.15 473.15 100.0
run             5000000    # 5 ns
unfix           4

fix             5 all npt temp 473.15 573.15 100.0 iso 1.0 1.0 1000.0
run             2000000    # 2 ns
unfix           5

fix             6 all nvt temp 573.15 573.15 100.0
run             5000000    # 5 ns
unfix           6

fix             7 all npt temp 573.15 673.15 100.0 iso 1.0 1.0 1000.0
run             2000000    # 2 ns
unfix           7

fix             8 all nvt temp 673.15 673.15 100.0
run             5000000    # 5 ns
unfix           8

fix             9 all npt temp 673.15 723.15 100.0 iso 1.0 1.0 1000.0
run             5000000    # 5 ns

write_data    datafin_1_6_anneal.lmp

I couldn’t attach the system data file, so these are the system parameters :

created by fftool

5504 atoms
5376 bonds
7552 angles
11520 dihedrals
46 atom types
49 bond types
73 angle types
135 dihedral types
0.000000 45.000000 xlo xhi
0.000000 45.000000 ylo yhi
0.000000 45.000000 zlo zhi

Masses

   1   14.007  # N00
   2    1.008  # H01
   3   12.011  # C02
   4   14.007  # N03
   5   12.011  # C04
   6   12.011  # C05
   7   12.011  # C06
   8   12.011  # C07
   9   12.011  # C08
  10   12.011  # C09
  11   12.011  # C0A
  12   12.011  # C0B
  13   12.011  # C0C
  14   12.011  # C0D
  15   12.011  # C0E
  16   12.011  # C0F
  17   14.007  # N0G
  18   12.011  # C0H
  19   14.007  # N0I
  20    1.008  # H0J
  21   12.011  # C0K
  22   12.011  # C0M
  23   12.011  # C0N
  24   12.011  # C0O
  25   12.011  # C0P
  26   12.011  # C0Q
  27    1.008  # H0R
  28    1.008  # H0S
  29    1.008  # H0T
  30    1.008  # H0U
  31    1.008  # H0V
  32    1.008  # H0W
  33    1.008  # H0X
  34    1.008  # H0Y
  35    1.008  # H0Z
  36    1.008  # H10
  37    1.008  # H11
  38    1.008  # H12
  39   30.974  # P00
  40   15.999  # O01
  41   15.999  # O02
  42   15.999  # O03
  43   15.999  # O04
  44    1.008  # H05
  45    1.008  # H06
  46    1.008  # H07

Bond Coeffs

   1   433.998566     1.010000  # H01-N00
   2   476.995698     1.343000  # C02-N00
   3   435.994264     1.374000  # C05-N00
   4   488.001912     1.335000  # N03-C02
   5   385.002390     1.460000  # C0K-C02
   6   410.002390     1.394000  # C04-N03
   7   469.000956     1.404000  # C05-C04
   8   469.000956     1.400000  # C09-C04
   9   469.000956     1.404000  # C06-C05
  10   469.000956     1.400000  # C07-C06
  11   367.005258     1.080000  # H0R-C06
  12   469.000956     1.400000  # C08-C07
  13   367.005258     1.080000  # H0S-C07
  14   469.000956     1.400000  # C09-C08
  15   385.002390     1.460000  # C0A-C08
  16   367.005258     1.080000  # H0T-C09
  17   469.000956     1.400000  # C0B-C0A
  18   469.000956     1.400000  # C0F-C0A
  19   469.000956     1.400000  # C0C-C0B
  20   367.005258     1.080000  # H0U-C0B
  21   469.000956     1.404000  # C0D-C0C
  22   367.005258     1.080000  # H0V-C0C
  23   469.000956     1.404000  # C0E-C0D
  24   435.994264     1.374000  # N0I-C0D
  25   469.000956     1.400000  # C0F-C0E
  26   410.002390     1.394000  # N0G-C0E
  27   367.005258     1.080000  # H0W-C0F
  28   488.001912     1.335000  # C0H-N0G
  29   476.995698     1.343000  # N0I-C0H
  30   367.005258     1.080000  # H0X-C0H
  31   433.998566     1.010000  # H0J-N0I
  32   469.000956     1.400000  # C0M-C0K
  33   469.000956     1.400000  # C0Q-C0K
  34   469.000956     1.400000  # C0N-C0M
  35   367.005258     1.080000  # H0Y-C0M
  36   469.000956     1.400000  # C0O-C0N
  37   367.005258     1.080000  # H0Z-C0N
  38   469.000956     1.400000  # C0P-C0O
  39   367.005258     1.080000  # H10-C0O
  40   469.000956     1.400000  # C0Q-C0P
  41   367.005258     1.080000  # H11-C0P
  42   367.005258     1.080000  # H12-C0Q
  43   525.000000     1.480000  # O01-P00
  44   229.995220     1.610000  # O02-P00
  45   229.995220     1.610000  # O03-P00
  46   229.995220     1.610000  # O04-P00
  47   552.999522     0.945000  # H05-O02
  48   552.999522     0.945000  # H06-O03
  49   552.999522     0.945000  # H07-O04

Angle Coeffs

   1    35.002390   120.000000  # H01-N00-C02
   2    29.995220   125.800000  # H01-N00-C05
   3    70.004780   109.800000  # C02-N00-C05
   4    70.004780   120.000000  # N00-C02-N03
   5    70.004780   125.000000  # N00-C02-C0K
   6    70.004780   130.000000  # N03-C02-C0K
   7    70.004780   110.000000  # C02-N03-C04
   8    70.004780   111.000000  # N03-C04-C05
   9    63.001912   120.000000  # C05-C04-C09
  10    70.004780   108.700000  # N00-C05-C04
  11    85.002390   134.900000  # C04-C05-C06
  12    63.001912   120.000000  # C05-C06-C07
  13    35.002390   120.000000  # C05-C06-H0R
  14    35.002390   120.000000  # C07-C06-H0R
  15    63.001912   120.000000  # C06-C07-C08
  16    35.002390   120.000000  # C06-C07-H0S
  17    35.002390   120.000000  # C08-C07-H0S
  18    63.001912   120.000000  # C07-C08-C09
  19    63.001912   120.000000  # C07-C08-C0A
  20    63.001912   120.000000  # C09-C08-C0A
  21    63.001912   120.000000  # C04-C09-C08
  22    35.002390   120.000000  # C04-C09-H0T
  23    35.002390   120.000000  # C08-C09-H0T
  24    63.001912   120.000000  # C08-C0A-C0B
  25    63.001912   120.000000  # C08-C0A-C0F
  26    63.001912   120.000000  # C0B-C0A-C0F
  27    63.001912   120.000000  # C0A-C0B-C0C
  28    35.002390   120.000000  # C0A-C0B-H0U
  29    35.002390   120.000000  # C0C-C0B-H0U
  30    63.001912   120.000000  # C0B-C0C-C0D
  31    35.002390   120.000000  # C0B-C0C-H0V
  32    35.002390   120.000000  # C0D-C0C-H0V
  33    85.002390   134.900000  # C0C-C0D-C0E
  34    70.004780   108.700000  # C0E-C0D-N0I
  35    63.001912   120.000000  # C0D-C0E-C0F
  36    70.004780   111.000000  # C0D-C0E-N0G
  37    63.001912   120.000000  # C0A-C0F-C0E
  38    35.002390   120.000000  # C0A-C0F-H0W
  39    35.002390   120.000000  # C0E-C0F-H0W
  40    70.004780   110.000000  # C0E-N0G-C0H
  41    70.004780   120.000000  # N0G-C0H-N0I
  42    35.002390   120.000000  # N0G-C0H-H0X
  43    35.002390   120.000000  # N0I-C0H-H0X
  44    70.004780   109.800000  # C0D-N0I-C0H
  45    29.995220   125.800000  # C0D-N0I-H0J
  46    35.002390   120.000000  # C0H-N0I-H0J
  47    63.001912   120.000000  # C02-C0K-C0M
  48    63.001912   120.000000  # C02-C0K-C0Q
  49    63.001912   120.000000  # C0M-C0K-C0Q
  50    63.001912   120.000000  # C0K-C0M-C0N
  51    35.002390   120.000000  # C0K-C0M-H0Y
  52    35.002390   120.000000  # C0N-C0M-H0Y
  53    63.001912   120.000000  # C0M-C0N-C0O
  54    35.002390   120.000000  # C0M-C0N-H0Z
  55    35.002390   120.000000  # C0O-C0N-H0Z
  56    63.001912   120.000000  # C0N-C0O-C0P
  57    35.002390   120.000000  # C0N-C0O-H10
  58    35.002390   120.000000  # C0P-C0O-H10
  59    63.001912   120.000000  # C0O-C0P-C0Q
  60    35.002390   120.000000  # C0O-C0P-H11
  61    35.002390   120.000000  # C0Q-C0P-H11
  62    63.001912   120.000000  # C0K-C0Q-C0P
  63    35.002390   120.000000  # C0K-C0Q-H12
  64    35.002390   120.000000  # C0P-C0Q-H12
  65   100.000000   108.200000  # O01-P00-O02
  66   100.000000   108.200000  # O01-P00-O03
  67   100.000000   108.200000  # O01-P00-O04
  68    45.004780   102.600000  # O02-P00-O03
  69    45.004780   102.600000  # O02-P00-O04
  70    45.004780   102.600000  # O03-P00-O04
  71    54.995220   108.500000  # P00-O02-H05
  72    54.995220   108.500000  # P00-O03-H06
  73    54.995220   108.500000  # P00-O04-H07

Dihedral Coeffs

   1     0.000000     5.000000     0.000000     0.000000  # N03-C02-N00-H01
   2     0.000000     5.000000     0.000000     0.000000  # C0K-C02-N00-H01
   3     0.000000    10.000000     0.000000     0.000000  # C05-N00-C02-N03
   4     0.000000     0.000000     0.000000     0.000000  # C0K-C02-N00-C05
   5     0.000000     5.000000     0.000000     0.000000  # C04-C05-N00-H01
   6     0.000000     5.000000     0.000000     0.000000  # C06-C05-N00-H01
   7     0.000000     7.250000     0.000000     0.000000  # C04-C05-N00-C02
   8     0.000000     7.250000     0.000000     0.000000  # C06-C05-N00-C02
   9     0.000000    10.000000     0.000000     0.000000  # C04-N03-C02-N00
  10     0.000000     7.250000     0.000000     0.000000  # C0K-C02-N03-C04
  11     0.000000     2.169933     0.000000     0.000000  # C0M-C0K-C02-N00
  12     0.000045     0.999543     0.035239    -0.254671  # C0Q-C0K-C02-N00
  13     0.000000     2.169933     0.000000     0.000000  # C0M-C0K-C02-N03
  14     0.000000     2.169933     0.000000     0.000000  # C0Q-C0K-C02-N03
  15     0.000000     7.250000     0.000000     0.000000  # C05-C04-N03-C02
  16     0.000000     7.250000     0.000000     0.000000  # C09-C04-N03-C02
  17     0.000000     2.169933     0.000000     0.000000  # N03-C04-C05-N00
  18     0.000000     2.169933     0.000000     0.000000  # C06-C05-C04-N03
  19     0.000000     7.250000     0.000000     0.000000  # C09-C04-C05-N00
  20     0.000000     2.169933     0.000000     0.000000  # C09-C04-C05-C06
  21     0.000000     2.169933     0.000000     0.000000  # C08-C09-C04-N03
  22     0.000000     7.250000     0.000000     0.000000  # H0T-C09-C04-N03
  23     0.000000     7.250000     0.000000     0.000000  # C08-C09-C04-C05
  24     0.000000     7.250000     0.000000     0.000000  # H0T-C09-C04-C05
  25     0.000000     7.000000     0.000000     0.000000  # C07-C06-C05-N00
  26     0.000000     7.250000     0.000000     0.000000  # H0R-C06-C05-N00
  27     0.000000     7.000000     0.000000     0.000000  # C07-C06-C05-C04
  28     0.000000     7.250000     0.000000     0.000000  # H0R-C06-C05-C04
  29     0.000000     7.250000     0.000000     0.000000  # C08-C07-C06-C05
  30     0.000000     7.250000     0.000000     0.000000  # H0S-C07-C06-C05
  31     0.000000     7.250000     0.000000     0.000000  # H0R-C06-C07-C08
  32     0.000000     7.250000     0.000000     0.000000  # H0S-C07-C06-H0R
  33     0.000000     7.250000     0.000000     0.000000  # C09-C08-C07-C06
  34     0.000000     7.250000     0.000000     0.000000  # C0A-C08-C07-C06
  35     0.000000     7.250000     0.000000     0.000000  # H0S-C07-C08-C09
  36     0.000000     7.250000     0.000000     0.000000  # H0S-C07-C08-C0A
  37     0.000000     7.250000     0.000000     0.000000  # C07-C08-C09-C04
  38     0.000000     7.250000     0.000000     0.000000  # H0T-C09-C08-C07
  39     0.000000     7.250000     0.000000     0.000000  # C0A-C08-C09-C04
  40     0.000000     7.250000     0.000000     0.000000  # H0T-C09-C08-C0A
  41     0.000000     2.169933     0.000000     0.000000  # C0B-C0A-C08-C07
  42     0.956023    -0.659133     0.000000   -21.510516  # C0F-C0A-C08-C07
  43     0.000000     2.169933     0.000000     0.000000  # C0B-C0A-C08-C09
  44     0.000000     2.169933     0.000000     0.000000  # C0F-C0A-C08-C09
  45     0.000000     7.250000     0.000000     0.000000  # C0C-C0B-C0A-C08
  46     0.000000     7.250000     0.000000     0.000000  # H0U-C0B-C0A-C08
  47     0.000000     7.250000     0.000000     0.000000  # C0F-C0A-C0B-C0C
  48     0.000000     7.250000     0.000000     0.000000  # H0U-C0B-C0A-C0F
  49     0.000000     7.250000     0.000000     0.000000  # C0E-C0F-C0A-C08
  50     0.000000     7.250000     0.000000     0.000000  # H0W-C0F-C0A-C08
  51     0.000000     7.250000     0.000000     0.000000  # C0E-C0F-C0A-C0B
  52     0.000000     7.250000     0.000000     0.000000  # H0W-C0F-C0A-C0B
  53     0.000000     7.250000     0.000000     0.000000  # C0D-C0C-C0B-C0A
  54     0.000000     7.250000     0.000000     0.000000  # H0V-C0C-C0B-C0A
  55     0.000000     7.250000     0.000000     0.000000  # H0U-C0B-C0C-C0D
  56     0.000000     7.250000     0.000000     0.000000  # H0V-C0C-C0B-H0U
  57     0.000000     7.000000     0.000000     0.000000  # C0E-C0D-C0C-C0B
  58     0.000000     7.000000     0.000000     0.000000  # N0I-C0D-C0C-C0B
  59     0.000000     7.250000     0.000000     0.000000  # H0V-C0C-C0D-C0E
  60     0.000000     7.250000     0.000000     0.000000  # H0V-C0C-C0D-N0I
  61     0.000000     2.169933     0.000000     0.000000  # C0F-C0E-C0D-C0C
  62     0.000000     2.169933     0.000000     0.000000  # N0G-C0E-C0D-C0C
  63     0.000000     7.250000     0.000000     0.000000  # N0I-C0D-C0E-C0F
  64     0.000000     2.169933     0.000000     0.000000  # N0I-C0D-C0E-N0G
  65     0.000000     7.250000     0.000000     0.000000  # C0H-N0I-C0D-C0C
  66     0.000000     5.000000     0.000000     0.000000  # H0J-N0I-C0D-C0C
  67     0.000000     7.250000     0.000000     0.000000  # C0H-N0I-C0D-C0E
  68     0.000000     5.000000     0.000000     0.000000  # H0J-N0I-C0D-C0E
  69     0.000000     7.250000     0.000000     0.000000  # C0D-C0E-C0F-C0A
  70     0.000000     7.250000     0.000000     0.000000  # H0W-C0F-C0E-C0D
  71     0.000000     2.169933     0.000000     0.000000  # N0G-C0E-C0F-C0A
  72     0.000000     7.250000     0.000000     0.000000  # H0W-C0F-C0E-N0G
  73     0.000000     7.250000     0.000000     0.000000  # C0H-N0G-C0E-C0D
  74     0.000000     7.250000     0.000000     0.000000  # C0H-N0G-C0E-C0F
  75     0.000000    10.000000     0.000000     0.000000  # N0I-C0H-N0G-C0E
  76     0.000000    10.000000     0.000000     0.000000  # H0X-C0H-N0G-C0E
  77     0.000000    10.000000     0.000000     0.000000  # N0G-C0H-N0I-C0D
  78     0.000000     5.000000     0.000000     0.000000  # H0J-N0I-C0H-N0G
  79     0.000000    10.000000     0.000000     0.000000  # H0X-C0H-N0I-C0D
  80     0.000000    10.000000     0.000000     0.000000  # H0X-C0H-N0I-H0J
  81     0.000000     7.250000     0.000000     0.000000  # C0N-C0M-C0K-C02
  82     0.000000     7.250000     0.000000     0.000000  # H0Y-C0M-C0K-C02
  83     0.000000     7.250000     0.000000     0.000000  # C0Q-C0K-C0M-C0N
  84     0.000000     7.250000     0.000000     0.000000  # H0Y-C0M-C0K-C0Q
  85     0.000000     7.250000     0.000000     0.000000  # C0P-C0Q-C0K-C02
  86     0.000000     7.250000     0.000000     0.000000  # H12-C0Q-C0K-C02
  87     0.000000     7.250000     0.000000     0.000000  # C0P-C0Q-C0K-C0M
  88     0.000000     7.250000     0.000000     0.000000  # H12-C0Q-C0K-C0M
  89     0.000000     7.250000     0.000000     0.000000  # C0O-C0N-C0M-C0K
  90     0.000000     7.250000     0.000000     0.000000  # H0Z-C0N-C0M-C0K
  91     0.000000     7.250000     0.000000     0.000000  # H0Y-C0M-C0N-C0O
  92     0.000000     7.250000     0.000000     0.000000  # H0Z-C0N-C0M-H0Y
  93     0.000000     7.250000     0.000000     0.000000  # C0P-C0O-C0N-C0M
  94     0.000000     7.250000     0.000000     0.000000  # H10-C0O-C0N-C0M
  95     0.000000     7.250000     0.000000     0.000000  # H0Z-C0N-C0O-C0P
  96     0.000000     7.250000     0.000000     0.000000  # H10-C0O-C0N-H0Z
  97     0.000000     7.250000     0.000000     0.000000  # C0Q-C0P-C0O-C0N
  98     0.000000     7.250000     0.000000     0.000000  # H11-C0P-C0O-C0N
  99     0.000000     7.250000     0.000000     0.000000  # H10-C0O-C0P-C0Q
 100     0.000000     7.250000     0.000000     0.000000  # H11-C0P-C0O-H10
 101     0.000000     7.250000     0.000000     0.000000  # C0O-C0P-C0Q-C0K
 102     0.000000     7.250000     0.000000     0.000000  # H12-C0Q-C0P-C0O
 103     0.000000     7.250000     0.000000     0.000000  # H11-C0P-C0Q-C0K
 104     0.000000     7.250000     0.000000     0.000000  # H12-C0Q-C0P-H11
 105     0.000000     0.000000     0.000000     0.000000  # H05-O02-P00-O01
 106     0.000000     0.000000     0.000000     0.000000  # H05-O02-P00-O03
 107     0.000000     0.000000     0.000000     0.000000  # H05-O02-P00-O04
 108     0.000000     0.000000     0.000000     0.000000  # H06-O03-P00-O01
 109     0.000000     0.000000     0.000000     0.000000  # H06-O03-P00-O02
 110     0.000000     0.000000     0.000000     0.000000  # H06-O03-P00-O04
 111     0.000000     0.000000     0.000000     0.000000  # H07-O04-P00-O01
 112     0.000000     0.000000     0.000000     0.000000  # H07-O04-P00-O02
 113     0.000000     0.000000     0.000000     0.000000  # H07-O04-P00-O03
 114     0.000000     2.500000     0.000000     0.000000  # H01-C02-N00-C05
 115     0.000000     2.500000     0.000000     0.000000  # N00-N03-C02-C0K
 116     0.000000     2.500000     0.000000     0.000000  # N03-C05-C04-C09
 117     0.000000     2.500000     0.000000     0.000000  # N00-C04-C05-C06
 118     0.000000     2.500000     0.000000     0.000000  # C05-C07-C06-H0R
 119     0.000000     2.500000     0.000000     0.000000  # C06-C08-C07-H0S
 120     0.000000     2.500000     0.000000     0.000000  # C07-C09-C08-C0A
 121     0.000000     2.500000     0.000000     0.000000  # C04-C08-C09-H0T
 122     0.000000     2.500000     0.000000     0.000000  # C08-C0B-C0A-C0F
 123     0.000000     2.500000     0.000000     0.000000  # C0A-C0C-C0B-H0U
 124     0.000000     2.500000     0.000000     0.000000  # C0B-C0D-C0C-H0V
 125     0.000000     2.500000     0.000000     0.000000  # C0C-C0E-C0D-N0I
 126     0.000000     2.500000     0.000000     0.000000  # C0D-C0F-C0E-N0G
 127     0.000000     2.500000     0.000000     0.000000  # C0A-C0E-C0F-H0W
 128     0.000000     2.500000     0.000000     0.000000  # N0G-N0I-C0H-H0X
 129     0.000000     2.500000     0.000000     0.000000  # C0D-C0H-N0I-H0J
 130     0.000000     2.500000     0.000000     0.000000  # C02-C0M-C0K-C0Q
 131     0.000000     2.500000     0.000000     0.000000  # C0K-C0N-C0M-H0Y
 132     0.000000     2.500000     0.000000     0.000000  # C0M-C0O-C0N-H0Z
 133     0.000000     2.500000     0.000000     0.000000  # C0N-C0P-C0O-H10
 134     0.000000     2.500000     0.000000     0.000000  # C0O-C0Q-C0P-H11
 135     0.000000     2.500000     0.000000     0.000000  # C0K-C0P-C0Q-H12M

Could please help me to fix this issue to run the simulation correctly?

Thank you in advance.

2

Have you looked at what the LAMMPS manual has to say about it (5.2. Errors and warnings details — LAMMPS documentation) or what other discussions of the same kind of error message have lead to before?

3

Yes I did, I’ve tried some solutions: reducing timestep to 0.5, increase Pdamp, redo the construction of the whole system, increasing simulation steps…

After doing some modifications in the input, other issues appear like out of range atoms or dihedrals or when I added to the input “fix shake” command this happens: warning: shake determinant < 0.0 (src/rigid/fix_shake.cpp:1859)

Could you please tell me what would be the root problem within the input or the system? And what solution I can follow?

Thank you,

And also what I noticed that my system breaks when T arriving at 450-500 K

4

You are doing a complex task and this can fail at multiple stages:

  • the atom classification and atom type assignment
  • the bond assignment and general bond topology generation
  • the translation of the geometry into a simulation system
  • the assignment of per-atom charges
  • close contacts or overlapping atom positions

Also, the methodology, i.e. choice of force field or the specific set of simulation parameters can be a problem. It is often a problem to use fix npt too soon when the system is too far from equilibrium.

Without fix shake using a 1fs timestep is far too large.
Even 0.5fs is aggressive and can only work for well equilibrated systems.
The fact that you get the “determinant error” with fix shake is an hint that there could be a problem with your bond topology. It is a symptom that you are either trying to constrain a linear chain of atoms (two bonds and an angle) or have a cluster (multiple bonds connected to the same atom) where the shake equations cannot converge (the atom positions are too far away too fulfill all constraints at the same time).

A good strategy is usually to try with a (much) smaller system; small enough so that you can manually verify that your data file and its contained bond topology and force field assignments are correct. Sometimes, you can just temporarily increase the force constants for bonded interactions by one or more order of magnitudes during minimization. Sometimes, you need to alternate between a few steps of MD and multiple minimizations. However, if that succeeds, then your general process if creating the initial geometry is flawed.

Also, you should make certain to have a recent LAMMPS version. With that you can use fix shake during minimization and it apply strong restraint forces during minimization automatically.

Finally, it can help to carefully visualize what you do at each step.

Bottom line, there is rarely a single “do this, not that” kind of solution and it is not possible to tell from remote with limited information to make a proper assessment of what is going wrong.

1 Like
5

Thank you very much for your explanation and guidance, I’ll try to equilibrate more my system using nvt but first I’ll check again my system data file if there are any contradiction in force field parameters.

6

Here are two suggestions for what I usually do to make some simple assessments of a system.

Before the first minimize or run command, I insert the commands:

delete_atoms   overlap 0.5 all all
compute        pe all pe/atom
run            0 post no
quit

Then I load the input into LAMMPS-GUI and run it (very quick since there is only one step)
and look at the log file for a line talking about deleted atoms:

peptide-deleted
peptide-deleted599×512 58.5 KB

No deleted atoms here, thus no problem (after all it is a pre-equilibrated example from the LAMMPS examples folder).

Then I open the ImageViewer window and open the Atoms/Bonds dialog to select coloring of the atoms by the pe/atom compute “c_pe”. Most of the (water) atoms have average potential energy, so no problem there either.

peptide-pe-all
peptide-pe-all1083×777 192 KB

Finally, I tell it to render only the atoms in the peptide group and zoom in a bit.

image
image600×600 78.6 KB

Since this uses a blue-white-red map (BWR) the blue atoms have the lowest potential energy and the red atoms the highest. The latter are backbone atoms, which makes sense and this also looks all good. If you had some “hotspot” in your geometry, you would see it. Since you can tell compute pe/atom to selectively only show the potential energy for either non-bonded, bonded, or kspace interactions, you can also track down where specific issues are. E.g. with some bad bond topology data, you may have very high bonded potential energy.

1 Like