lammps minimization error

Govind_Reddy · August 3, 2016, 1:57pm

Dear users,

I tried to build and LAMMPS dynamic properties of the “F-substituted p3ht” polymer using "polymatic"

But i get an error " LAMMPS energy minimization did not complete properly"

setting section created by “moltamplate” using GAFF force field parameters.

The input files are given below

1) p3ht.lt (Inpute file for “moltemplate”)

import “gaff.lt”

# From “gaff.lt”:
# @atom:cc1 # Sp2 carbons in non-pure aromatic systems
# @atom:cc4 # Sp2 carbons in non-pure aromatic systems
# @atom:cd # Sp2 carbons in non-pure aromatic systems, identical to cc
# @atom:hc # H bonded to aliphatic carbon without electrwd. group
# @atom:ss # Sp3 S in thio-ester and thio-ether
# @atom:f # Fluorine
# @atom:c3 # Sp3 C(c3)

f-p3ht inherits GAFF {

# atomID molID atomType charge X Y Z
write(“Data Atoms”) {
$atom:C1 $mol @atom:cc1 -0.251330 -2.992197 -0.970903 0.136447
$atom:C2 $mol @atom:cd 0.285577 -1.615590 -0.967778 0.177626
$atom:C3 $mol @atom:cd 0.072106 -1.087636 0.351460 -0.000810
$atom:C4 $mol @atom:cc4 -0.233082 -2.091681 1.279310 -0.167091
$atom:S5 $mol @atom:ss 0.358712 -3.603153 0.566381 -0.107759
$atom:C6 $mol @atom:c3 -0.227398 0.420925 0.661048 -0.001617
$atom:C7 $mol @atom:c3 -0.182741 0.966860 0.621737 1.402630
$atom:H8 $mol @atom:hc 0.106497 0.573831 1.670184 -0.455183
$atom:H9 $mol @atom:hc 0.118755 0.935600 -0.092766 -0.645282
$atom:C10 $mol @atom:c3 -0.174215 2.443562 0.921000 1.437669
$atom:H11 $mol @atom:hc 0.101399 0.418809 1.367108 2.038043
$atom:H12 $mol @atom:hc 0.109635 0.779590 -0.391022 1.848640
$atom:H13 $mol @atom:hc 0.091229 3.010968 0.173859 0.831591
$atom:H14 $mol @atom:hc 0.090014 2.649173 1.936898 1.021521
$atom:C15 $mol @atom:c3 -0.167890 2.967827 0.872695 2.884878
$atom:C16 $mol @atom:c3 -0.174529 4.444995 1.169801 2.919563
$atom:H17 $mol @atom:hc 0.091411 2.760749 -0.142680 3.301520
$atom:H18 $mol @atom:hc 0.089724 2.401503 1.620895 3.490604
$atom:C19 $mol @atom:c3 -0.317959 4.991043 1.130469 4.323742
$atom:H20 $mol @atom:hc 0.092143 4.991724 0.423248 2.284398
$atom:H21 $mol @atom:hc 0.091541 4.633626 2.182023 2.472908
$atom:H22 $mol @atom:hc 0.100285 6.085170 1.353308 4.322982
$atom:H23 $mol @atom:hc 0.102390 4.477507 1.885499 4.966947
$atom:H24 $mol @atom:hc 0.102972 4.836601 0.121813 4.777905
$atom:F25 $mol @atom:f -0.275247 -0.837002 -2.055267 0.361113
}

write(“Data Bond List”) {
$bond:C1C2 $atom:C1 $atom:C2
$bond:C2C3 $atom:C2 $atom:C3
$bond:C3C4 $atom:C3 $atom:C4
$bond:C4S5 $atom:C4 $atom:S5
$bond:C1S5 $atom:C1 $atom:S5
$bond:C2F25 $atom:C2 $atom:F25
$bond:C3C6 $atom:C3 $atom:C6
$bond:C6C7 $atom:C6 $atom:C7
$bond:C7C10 $atom:C7 $atom:C10
$bond:C10C15 $atom:C10 $atom:C15
$bond:C15C16 $atom:C15 $atom:C16
$bond:C16C19 $atom:C16 $atom:C19
$bond:C6H8 $atom:C6 $atom:H8
$bond:C6H9 $atom:C6 $atom:H9
$bond:C7H11 $atom:C7 $atom:H11
$bond:C7H12 $atom:C7 $atom:H12
$bond:C10H13 $atom:C10 $atom:H13
$bond:C10H14 $atom:C10 $atom:H14
$bond:C15H18 $atom:C15 $atom:H18
$bond:C15H17 $atom:C15 $atom:H17
$bond:C16H20 $atom:C16 $atom:H20
$bond:C16H21 $atom:C16 $atom:H21
$bond:C19H23 $atom:C19 $atom:H23
$bond:C19H24 $atom:C19 $atom:H24
$bond:C19H22 $atom:C19 atom:H22 } } # F-p3ht **2 ) min.lmps** #------------init section------------------ units real atom_style full bond_style hybrid harmonic angle_style hybrid harmonic dihedral_style hybrid fourier improper_style hybrid cvff pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 kspace_style pppm 0.0001 pair_modify mix arithmetic special_bonds amber # Data file input read_data data.lmps (= pack.lmps by polymatic) #-------------------setting section--------------- pair_coeff 1 1 lj/charmm/coul/long 0.0860 3.39966950842 # OPLS pair_coeff 2 2 lj/charmm/coul/long 0.0860 3.39966950842 # OPLS pair_coeff 3 3 lj/charmm/coul/long 0.0860 3.39966950842 # OPLS pair_coeff 4 4 lj/charmm/coul/long 0.0860 3.39966950842 # OPLS pair_coeff 5 5 lj/charmm/coul/long 0.0860 3.39966950842 # OPLS pair_coeff 6 6 lj/charmm/coul/long 0.0157 2.64953278775 # OPLS pair_coeff 7 7 lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's pair_coeff 9 9 lj/charmm/coul/long 0.1094 3.39966950842 # OPLS pair_coeff 8 8 lj/charmm/coul/long 0.061 3.11814551349 # Gough et al. JCC 13,(1992),963. bond_coeff 1 harmonic 303.1 1.5350 # SOURCE1 14664 0.0048 bond_coeff 2 harmonic 337.3 1.0920 # SOURCE3 2815 0.0059 bond_coeff 3 harmonic 337.3 1.4990 # SOURCE3 50 0.0096 bond_coeff 4 harmonic 418.3 1.4290 # SOURCE1 740 0.0069 bond_coeff 5 harmonic 504.0 1.3710 # SOURCE3 523 0.0217 bond_coeff 6 harmonic 504.0 1.3710 # SOURCE3 523 0.0217 bond_coeff 7 harmonic 504.0 1.3710 # SOURCE3 523 0.0217 bond_coeff 8 harmonic 504.0 1.3710 # SOURCE3 523 0.0217 bond_coeff 9 harmonic 279.3 1.7370 # SOURCE3 52 0.0194 bond_coeff 10 harmonic 279.3 1.7370 # SOURCE3 52 0.0194 bond_coeff 11 harmonic 279.3 1.7370 # SOURCE3 52 0.0194 bond_coeff 12 harmonic 279.3 1.7370 # SOURCE3 52 0.0194 bond_coeff 13 harmonic 418.3 1.4290 # SOURCE1 740 0.0069 bond_coeff 14 harmonic 368.6 1.3401 # NEW 24 angle_coeff 1 harmonic 63.21 110.63 # SOURCE3 507 2.7845 angle_coeff 2 harmonic 46.37 110.05 # SOURCE3 2092 0.6991 angle_coeff 3 harmonic 39.43 108.35 # SOURCE3 2380 0.9006 angle_coeff 4 harmonic 63.58 111.89 # CORR 700 angle_coeff 5 harmonic 47.20 110.86 # SOURCE3 85 1.0276 angle_coeff 6 harmonic 68.16 114.19 # SOURCE3 517 6.5960 angle_coeff 7 harmonic 62.45 120.12 # CORR 31 angle_coeff 8 harmonic 65.44 111.55 # CORR 884 angle_coeff 9 harmonic 65.44 111.55 # CORR 884 angle_coeff 10 harmonic 65.44 111.55 # CORR 884 angle_coeff 11 harmonic 65.44 111.55 # CORR 884 angle_coeff 12 harmonic 64.81 119.45 # SOURCE3 35 8.2040 angle_coeff 13 harmonic 64.81 119.45 # SOURCE3 35 8.2040 angle_coeff 14 harmonic 64.66 115.97 # SOURCE3 4 3.0507 angle_coeff 15 harmonic 68.16 114.19 # SOURCE3 517 6.5960 angle_coeff 16 harmonic 68.16 114.19 # SOURCE3 517 6.5960 angle_coeff 17 harmonic 68.16 114.19 # SOURCE3 517 6.5960 angle_coeff 18 harmonic 68.16 114.19 # SOURCE3 517 6.5960 angle_coeff 19 harmonic 67.01 89.91 # SOURCE3 11 2.2164 angle_coeff 20 harmonic 67.01 89.91 # SOURCE3 11 2.2164 angle_coeff 21 harmonic 66.35 119.41 # NEW 7 angle_coeff 22 harmonic 67.42 121.08 # NEW 28 angle_coeff 23 harmonic 67.42 121.08 # NEW 28 dihedral_coeff 1 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 2 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 3 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 4 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 5 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 6 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 7 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 8 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 9 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 10 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 11 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 12 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 13 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 14 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 15 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 16 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 17 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 18 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 19 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 20 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 21 fourier 1 4.0 2 180.0 # statistic value of parm94 dihedral_coeff 22 fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 dihedral_coeff 23 fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 dihedral_coeff 24 fourier 1 0.0 3 0.0 # same as X-c3-ca-X dihedral_coeff 25 fourier 1 0.0 3 0.0 # same as X-c3-ca-X dihedral_coeff 26 fourier 1 0.0 3 0.0 # same as X-c3-ca-X dihedral_coeff 27 fourier 1 0.0 3 0.0 # same as X-c3-ca-X dihedral_coeff 28 fourier 1 0.0 3 0.0 # same as X-c3-ca-X dihedral_coeff 29 fourier 1 0.0 3 0.0 # same as X-c3-ca-X dihedral_coeff 30 fourier 1 0.15 3 0.0 # Junmei et al, 1999 dihedral_coeff 31 fourier 1 0.16 3 0.0 # Junmei et al, 1999 dihedral_coeff 32 fourier 3 0.18 3 0.0 0.25 2 180.0 0.2 1 180.0 # Junmei et al, 1999 # Minimization Step min_style cg minimize 1e-25 1e-25 500000 1000000 # Data file output write_data min.lmps **OUTPUTE FILES** 1) **log.lmps as follows** LAMMPS (7 Dec 2015) WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:90) using 1 OpenMP thread(s) per MPI task package omp 0 using multi-threaded neighbor list subroutines package omp 1 using multi-threaded neighbor list subroutines #------------init section------------------ units real atom_style full bond_style hybrid harmonic angle_style hybrid harmonic dihedral_style hybrid fourier improper_style hybrid cvff pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 kspace_style pppm 0.0001 pair_modify mix arithmetic special_bonds amber # Data file input read_data data.lmps orthogonal box = (0 0 0) to (20 20 20) 2 by 2 by 4 MPI processor grid reading atoms ... 75 atoms scanning bonds ... 3 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 9 = max dihedrals/atom reading bonds ... 75 bonds reading angles ... 135 angles reading dihedrals ... 177 dihedrals 4 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 12 = max # of 1-4 neighbors 16 = max # of special neighbors #-------------------setting section--------------- pair_coeff 1 1 lj/charmm/coul/long 0.0860 3.39966950842 # OPLS pair_coeff 2 2 lj/charmm/coul/long 0.0860 3.39966950842 # OPLS pair_coeff 3 3 lj/charmm/coul/long 0.0860 3.39966950842 # OPLS pair_coeff 4 4 lj/charmm/coul/long 0.0860 3.39966950842 # OPLS pair_coeff 5 5 lj/charmm/coul/long 0.0860 3.39966950842 # OPLS pair_coeff 6 6 lj/charmm/coul/long 0.0157 2.64953278775 # OPLS pair_coeff 7 7 lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's pair_coeff 9 9 lj/charmm/coul/long 0.1094 3.39966950842 # OPLS pair_coeff 8 8 lj/charmm/coul/long 0.061 3.11814551349 # Gough et al. JCC 13,(1992),963. bond_coeff 1 harmonic 303.1 1.5350 # SOURCE1 14664 0.0048 bond_coeff 2 harmonic 337.3 1.0920 # SOURCE3 2815 0.0059 bond_coeff 3 harmonic 337.3 1.4990 # SOURCE3 50 0.0096 bond_coeff 4 harmonic 418.3 1.4290 # SOURCE1 740 0.0069 bond_coeff 5 harmonic 504.0 1.3710 # SOURCE3 523 0.0217 bond_coeff 6 harmonic 504.0 1.3710 # SOURCE3 523 0.0217 bond_coeff 7 harmonic 504.0 1.3710 # SOURCE3 523 0.0217 bond_coeff 8 harmonic 504.0 1.3710 # SOURCE3 523 0.0217 bond_coeff 9 harmonic 279.3 1.7370 # SOURCE3 52 0.0194 bond_coeff 10 harmonic 279.3 1.7370 # SOURCE3 52 0.0194 bond_coeff 11 harmonic 279.3 1.7370 # SOURCE3 52 0.0194 bond_coeff 12 harmonic 279.3 1.7370 # SOURCE3 52 0.0194 bond_coeff 13 harmonic 418.3 1.4290 # SOURCE1 740 0.0069 bond_coeff 14 harmonic 368.6 1.3401 # NEW 24 angle_coeff 1 harmonic 63.21 110.63 # SOURCE3 507 2.7845 angle_coeff 2 harmonic 46.37 110.05 # SOURCE3 2092 0.6991 angle_coeff 3 harmonic 39.43 108.35 # SOURCE3 2380 0.9006 angle_coeff 4 harmonic 63.58 111.89 # CORR 700 angle_coeff 5 harmonic 47.20 110.86 # SOURCE3 85 1.0276 angle_coeff 6 harmonic 68.16 114.19 # SOURCE3 517 6.5960 angle_coeff 7 harmonic 62.45 120.12 # CORR 31 angle_coeff 8 harmonic 65.44 111.55 # CORR 884 angle_coeff 9 harmonic 65.44 111.55 # CORR 884 angle_coeff 10 harmonic 65.44 111.55 # CORR 884 angle_coeff 11 harmonic 65.44 111.55 # CORR 884 angle_coeff 12 harmonic 64.81 119.45 # SOURCE3 35 8.2040 angle_coeff 13 harmonic 64.81 119.45 # SOURCE3 35 8.2040 angle_coeff 14 harmonic 64.66 115.97 # SOURCE3 4 3.0507 angle_coeff 15 harmonic 68.16 114.19 # SOURCE3 517 6.5960 angle_coeff 16 harmonic 68.16 114.19 # SOURCE3 517 6.5960 angle_coeff 17 harmonic 68.16 114.19 # SOURCE3 517 6.5960 angle_coeff 18 harmonic 68.16 114.19 # SOURCE3 517**[[email protected]... step_000]**

THIS IS THE last line executed in the log.lammps

Can you explain to me what the problem is and how I can resolve it?

Thanks in advance,

|

sjplimp · August 3, 2016, 2:13pm

This is not an error from LAMMPS itself is it?

" LAMMPS energy minimization did not complete properly"

Maybe you should ask the authors of your tool why and when

they flag that error?

Steve