LAMMPS (23 Jun 2022) # solvated ubiquitin molecule with AMOEBA force field units real boundary p p p atom_modify sort 0 0.0 atom_style amoeba bond_style class2 angle_style amoeba dihedral_style fourier improper_style amoeba # per-atom properties required by AMOEBA or HIPPO fix amtype all property/atom i_amtype ghost yes fix extra all property/atom i_amgroup d_redID d_pval ghost yes fix extra2 all property/atom i_polaxe d2_xyzaxis 3 fix pit all amoeba/pitorsion fix_modify pit energy yes fix bit all amoeba/bitorsion bitorsion.ubiquitin.data fix_modify bit energy yes # read data file read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions Reading data file ... orthogonal box = (0 0 0) to (54.99 41.91 41.91) 1 by 1 by 1 MPI processor grid reading atoms ... 9737 atoms scanning bonds ... 4 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 18 = max dihedrals/atom scanning impropers ... 3 = max impropers/atom reading bonds ... 6908 bonds reading angles ... 5094 angles reading dihedrals ... 3297 dihedrals reading impropers ... 651 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 4 = max # of 1-2 neighbors 9 = max # of 1-3 neighbors 19 = max # of 1-4 neighbors 21 = max # of special neighbors special bonds CPU = 0.004 seconds read_data CPU = 0.091 seconds pair_style amoeba pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05 Skipping section: AMOEBA Protein Force Field Atom Classes Skipping section: Torsion-Torsion Parameters Skipping section: Biopolymer Atom Type Conversions Reading potential file amoeba_ubiquitin.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0.5 0.5 0.5 special bond factors coul: 0.5 0.5 0.5 4 = max # of 1-2 neighbors 9 = max # of 1-3 neighbors 19 = max # of 1-4 neighbors 58 = max # of 1-5 neighbors 21 = max # of special neighbors special bonds CPU = 0.007 seconds # thermo output compute virial all pressure NULL virial thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] #dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz #dump_modify 1 sort id # dynamics fix 1 all nve thermo 1 run 10 AMOEBA force field settings hal: cut 12 taper 10.8 vscale 0 0 1 1 multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1 polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48 pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1 precondition: cut 4.5 Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 8 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair amoeba, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard AMOEBA group count: 3196 Per MPI rank memory allocation (min/avg/max) = 258.3 | 258.3 | 258.3 Mbytes Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6] 0 0 -35338.057 2856.5938 1955.5431 224.37609 65.00809 5101.5211 -30247.585 -6336.5196 -5795.4272 -6329.8149 -6884.3167 349.52657 77.164877 652.41925 1 29.61379 -35356.153 2037.3541 1840.7883 223.90217 64.293945 4166.3385 -30341.522 -6486.773 -6452.8463 -6841.5982 -7386.1106 311.38025 120.72605 545.35513 2 78.518242 -35383.65 825.39919 1538.3909 222.55095 62.191009 2648.5321 -30467.814 -5502.9841 -6410.2998 -6396.1829 -6937.8137 217.3515 210.76948 294.28051 3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776 4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224 5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369 6 118.24373 -36092.77 1166.179 815.59206 213.67399 44.022297 2239.4673 -30435.629 -1677.8051 -3988.2428 -2669.6848 -3247.7207 197.42472 285.87129 -162.35459 7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786 8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727 9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705 10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746 Loop time of 24.2102 on 1 procs for 10 steps with 9737 atoms Performance: 0.036 ns/day, 672.507 hours/ns, 0.413 timesteps/s 97.8% CPU use with 1 MPI tasks x no OpenMP threads AMOEBA timing breakdown: Init time: 0.0401664 0.17% Hal time: 7.62094 31.51% Mpole time: 2.44622 10.12% Induce time: 9.28925 38.41% Polar time: 4.78631 19.79% Total time: 24.1829 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 24.183 | 24.183 | 24.183 | 0.0 | 99.89 Bond | 0.016031 | 0.016031 | 0.016031 | 0.0 | 0.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.004396 | 0.004396 | 0.004396 | 0.0 | 0.02 Output | 0.0011692 | 0.0011692 | 0.0011692 | 0.0 | 0.00 Modify | 0.0044765 | 0.0044765 | 0.0044765 | 0.0 | 0.02 Other | | 0.001194 | | | 0.00 Nlocal: 9737 ave 9737 max 9737 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 31511 ave 31511 max 31511 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5.6393e+06 ave 5.6393e+06 max 5.6393e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5639296 Ave neighs/atom = 579.16155 Ave special neighs/atom = 3.1364897 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:27