Dear LAMMPS Users
I am trying to simulate a system of a metallic nanotube with a protein in an aqueous medium, however after 74ns, the following error appears: ERROR on proc 75: Bond atoms 142 143 missing on proc 75 at step 37423342 (…/ntopo_bond_partial .cpp: 64). Please, I require some idea of where my problem may be since the simulation is fine for many steps of time. The most important lines of the inputscript that I use are:
#===============================Settings =======================================================
neighbor 2 bin
neigh_modify every 1 delay 0 check yes
timestep 2.0 #(2 fs)
velocity all create 0.0 12345678 dist uniform
kspace_style pppm 1.0e-4
special_bonds charmm
#===============================Minization =====================================================
minimize 1.0e-4 1.0e-8 1000 10000
#============================== Radius of gyration =============================================
compute 4 fibril gyration
variable gyration equal c_4
#============================= Thermo ===========================================================
thermo 20000
thermo_style custom step temp press pe ke etotal ecoul epair lx ly lz vol v_InterEnergy v_gyration
#============================= Equilibration=====================================================
fix 1 all spring/self 10.0
fix 2 all nvt temp 300.0 300.0 $(5.0*dt)
run 500000 #(time of simulation = 2 fs x 500000 = 1000000fs → 1000ps → 1ns)
unfix 1
unfix 2
#============================= Production ========================================================
fix 10 water shake 0.0001 10 0 b 1 a 1
fix 11 all npt temp 300.0 300.0 $(5.0*dt) iso 1 1 1000
run 50000000 #(time of simulation = 2 fs x 50000000 = 100000000fs → 100000ps → 100ns)
Next I present part of the result of log.lammps
Step Temp Press PotEng KinEng TotEng E_coul E_pair Lx Ly Lz Volume v_InterEnergy v_gyration
…
36920000 299.69775 346.25617 -1915255.2 38834.473 -1876420.7 -705776.23 -1938886.4 63.304578 90.994284 75.298582 433746.55 -825.28158 13.815695
36940000 300.94522 34.560937 -1914937.4 38996.119 -1875941.2 -705069.04 -1938659 63.379591 91.102108 75.387808 435290.28 -855.65004 13.744695
36960000 299.05711 -37.150416 -1915016.9 38751.46 -1876265.4 -705742.43 -1938911.5 63.313212 91.006694 75.308852 433924.04 -838.84477 13.749175
36980000 298.59364 -267.25044 -1914750.6 38691.404 -1876059.2 -704566.88 -1938505.7 63.352286 91.06286 75.355329 434727.93 -871.66576 13.727032
37000000 298.34728 139.40008 -1915042.2 38659.481 -1876382.8 -706614.33 -1939092.8 63.341226 91.046963 75.342174 434500.29 -824.69798 13.754637
37020000 300.83975 55.114019 -1915281.8 38982.452 -1876299.4 -705935.62 -1939014.4 63.384306 91.108885 75.393416 435387.43 -781.81273 13.747822
37040000 300.85803 -361.12083 -1915382.4 38984.821 -1876397.6 -706175.73 -1939158.9 63.280444 90.959594 75.269875 433250.65 -807.89267 13.815207
37060000 300.69263 12.626786 -1915166.7 38963.388 -1876203.3 -706511.9 -1939070.8 63.366284 91.082981 75.371979 435016.17 -890.64396 13.744989
37080000 300.82085 -19.824162 -1915259.4 38980.003 -1876279.3 -705739.92 -1938941.5 63.322749 91.020403 75.320196 434120.16 -855.44474 13.749806
37100000 299.95395 -292.36728 -1914929.1 38867.671 -1876061.4 -705743.06 -1938997.4 63.28498 90.966113 75.275271 433343.82 -798.57846 13.7649
37120000 297.90888 236.07466 -1914953.1 38602.673 -1876350.4 -705862.76 -1938699.8 63.316707 91.011718 75.313009 433995.91 -881.77322 13.824688
37140000 299.50197 136.89385 -1915002 38809.104 -1876192.9 -705195.65 -1938835.2 63.33035 91.03133 75.329238 434276.52 -820.57223 13.740301
37160000 299.11619 291.80069 -1915134.7 38759.114 -1876375.5 -706036.98 -1938811.5 63.33151 91.032996 75.330617 434300.38 -770.70328 13.753886
37180000 299.56689 402.56895 -1915108.3 38817.516 -1876290.8 -705436.24 -1938610.7 63.389717 91.116663 75.399852 435498.94 -779.37707 13.802964
37200000 301.14717 -20.832882 -1915466.7 39022.287 -1876444.4 -705885.79 -1939144.5 63.339864 91.045005 75.340554 434472.26 -848.56446 13.717127
37220000 299.71697 -40.187015 -1914999 38836.964 -1876162.1 -705535.99 -1938702.4 63.378869 91.10107 75.386949 435275.4 -791.48461 13.653879
37240000 298.74847 9.5324732 -1915028.8 38711.466 -1876317.4 -706282.85 -1938950.9 63.275049 90.951839 75.263459 433139.86 -856.77682 13.714697
37260000 298.85557 187.40569 -1915428.3 38725.345 -1876703 -706074.27 -1939289.7 63.337038 91.040942 75.337192 434414.11 -820.68075 13.735903
37280000 301.85963 -221.20787 -1914773 39114.607 -1875658.4 -705006 -1938691.8 63.32483 91.023394 75.322671 434162.96 -819.39823 13.660091
37300000 301.06233 -119.23787 -1914950 39011.294 -1875938.7 -705928.34 -1938881.4 63.331132 91.032453 75.330167 434292.6 -858.38212 13.74013
37320000 303.61581 140.29859 -1915337.5 39342.171 -1875995.3 -705496.11 -1938947.4 63.310715 91.003106 75.305882 433872.71 -861.42601 13.723266
37340000 300.95954 -112.76187 -1915115.8 38997.975 -1876117.8 -705723.44 -1938982.1 63.308316 90.999657 75.303029 433823.39 -857.45557 13.725127
37360000 300.93558 -135.08166 -1915341.6 38994.87 -1876346.7 -705523.82 -1939083.3 63.336102 91.039597 75.336079 434394.85 -815.1576 13.734257
37380000 301.66166 8.0553032 -1915040.1 39088.955 -1875951.2 -705307.05 -1938822.8 63.33712 91.041061 75.33729 434415.8 -851.34099 13.786184
37400000 298.04593 337.37895 -1915289.5 38620.433 -1876669 -706133.86 -1939106.2 63.264311 90.936404 75.250686 432919.37 -854.17581 13.718676
37420000 298.55485 621.81307 -1915009.9 38686.377 -1876323.5 -706131.5 -1938848.6 63.277954 90.956014 75.266913 433199.51 -816.01161 13.686425
ERROR on proc 75: Bond atoms 142 143 missing on proc 75 at step 37423342 (…/ntopo_bond_partial.cpp:64)
Last command: run 50000000 #(time of simulation = 2 fs x 50000000 = 100000000fs → 100000ps → 100ns)
Sincerely
Eduardo