GROMACS version: 2019.5
GROMACS modification: Yes/No
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I am getting the following error, how do I fix it? i searched the internet for this but could’nt find a proper answer.
Full error:
NOTE 1 [file minim.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to 2147035080
Generated 339076 of the 339076 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 339076 of the 339076 1-4 parameter combinations
ERROR 1 [file gelatinitp.itp, line 142]:
No default Bond types
ERROR 2 [file gelatinitp.itp, line 185]:
No default Bond types
ERROR 3 [file gelatinitp.itp, line 187]:
No default Bond types
ERROR 4 [file gelatinitp.itp, line 188]:
No default Bond types
ERROR 5 [file gelatinitp.itp, line 189]:
No default Bond types
ERROR 6 [file gelatinitp.itp, line 231]:
No default Bond types
ERROR 7 [file gelatinitp.itp, line 263]:
No default Bond types
ERROR 8 [file gelatinitp.itp, line 478]:
No default Angle types
ERROR 9 [file gelatinitp.itp, line 484]:
No default Angle types
ERROR 10 [file gelatinitp.itp, line 485]:
Duplicate atom index (5) in angles
ERROR 11 [file gelatinitp.itp, line 485]:
No default Angle types
ERROR 12 [file gelatinitp.itp, line 500]:
Duplicate atom index (9) in angles
ERROR 13 [file gelatinitp.itp, line 500]:
No default Angle types
ERROR 14 [file gelatinitp.itp, line 532]:
Duplicate atom index (16) in angles
ERROR 15 [file gelatinitp.itp, line 532]:
No default Angle types
ERROR 16 [file gelatinitp.itp, line 564]:
No default Angle types
ERROR 17 [file gelatinitp.itp, line 567]:
No default Angle types
ERROR 18 [file gelatinitp.itp, line 568]:
No default Angle types
ERROR 19 [file gelatinitp.itp, line 569]:
No default Angle types
ERROR 20 [file gelatinitp.itp, line 570]:
No default Angle types
ERROR 21 [file gelatinitp.itp, line 571]:
No default Angle types
ERROR 22 [file gelatinitp.itp, line 572]:
No default Angle types
ERROR 23 [file gelatinitp.itp, line 573]:
No default Angle types
ERROR 24 [file gelatinitp.itp, line 574]:
No default Angle types
ERROR 25 [file gelatinitp.itp, line 575]:
Duplicate atom index (25) in angles
ERROR 26 [file gelatinitp.itp, line 575]:
No default Angle types
ERROR 27 [file gelatinitp.itp, line 576]:
No default Angle types
ERROR 28 [file gelatinitp.itp, line 577]:
No default Angle types
ERROR 29 [file gelatinitp.itp, line 578]:
No default Angle types
ERROR 30 [file gelatinitp.itp, line 579]:
No default Angle types
ERROR 31 [file gelatinitp.itp, line 581]:
No default Angle types
ERROR 32 [file gelatinitp.itp, line 582]:
Duplicate atom index (27) in angles
ERROR 33 [file gelatinitp.itp, line 582]:
No default Angle types
ERROR 34 [file gelatinitp.itp, line 597]:
Duplicate atom index (31) in angles
ERROR 35 [file gelatinitp.itp, line 597]:
No default Angle types
ERROR 36 [file gelatinitp.itp, line 627]:
Duplicate atom index (37) in angles
ERROR 37 [file gelatinitp.itp, line 630]:
Duplicate atom index (40) in angles
ERROR 38 [file gelatinitp.itp, line 630]:
No default Angle types
ERROR 39 [file gelatinitp.itp, line 644]:
No default Angle types
ERROR 40 [file gelatinitp.itp, line 651]:
No default Angle types
ERROR 41 [file gelatinitp.itp, line 654]:
No default Angle types
ERROR 42 [file gelatinitp.itp, line 655]:
No default Angle types
ERROR 43 [file gelatinitp.itp, line 656]:
No default Angle types
ERROR 44 [file gelatinitp.itp, line 657]:
No default Angle types
ERROR 45 [file gelatinitp.itp, line 663]:
Duplicate atom index (48) in angles
ERROR 46 [file gelatinitp.itp, line 663]:
No default Angle types
ERROR 47 [file gelatinitp.itp, line 678]:
Duplicate atom index (52) in angles
ERROR 48 [file gelatinitp.itp, line 678]:
No default Angle types
ERROR 49 [file gelatinitp.itp, line 694]:
No default Angle types
ERROR 50 [file gelatinitp.itp, line 710]:
Duplicate atom index (59) in angles
ERROR 51 [file gelatinitp.itp, line 710]:
No default Angle types
ERROR 52 [file gelatinitp.itp, line 713]:
No default Angle types
ERROR 53 [file gelatinitp.itp, line 717]:
No default Ryckaert-Bell. types
ERROR 54 [file gelatinitp.itp, line 718]:
No default Ryckaert-Bell. types
ERROR 55 [file gelatinitp.itp, line 721]:
No default Ryckaert-Bell. types
ERROR 56 [file gelatinitp.itp, line 724]:
No default Ryckaert-Bell. types
ERROR 57 [file gelatinitp.itp, line 725]:
No default Ryckaert-Bell. types
ERROR 58 [file gelatinitp.itp, line 790]:
No default Ryckaert-Bell. types
ERROR 59 [file gelatinitp.itp, line 792]:
No default Ryckaert-Bell. types
ERROR 60 [file gelatinitp.itp, line 793]:
No default Ryckaert-Bell. types
ERROR 61 [file gelatinitp.itp, line 794]:
No default Ryckaert-Bell. types
ERROR 62 [file gelatinitp.itp, line 795]:
No default Ryckaert-Bell. types
ERROR 63 [file gelatinitp.itp, line 796]:
No default Ryckaert-Bell. types
ERROR 64 [file gelatinitp.itp, line 797]:
No default Ryckaert-Bell. types
ERROR 65 [file gelatinitp.itp, line 798]:
No default Ryckaert-Bell. types
ERROR 66 [file gelatinitp.itp, line 799]:
No default Ryckaert-Bell. types
ERROR 67 [file gelatinitp.itp, line 800]:
No default Ryckaert-Bell. types
ERROR 68 [file gelatinitp.itp, line 801]:
No default Ryckaert-Bell. types
ERROR 69 [file gelatinitp.itp, line 802]:
No default Ryckaert-Bell. types
ERROR 70 [file gelatinitp.itp, line 803]:
No default Ryckaert-Bell. types
ERROR 71 [file gelatinitp.itp, line 804]:
No default Ryckaert-Bell. types
ERROR 72 [file gelatinitp.itp, line 805]:
Duplicate atom index (25) in dihedrals
ERROR 73 [file gelatinitp.itp, line 805]:
No default Ryckaert-Bell. types
ERROR 74 [file gelatinitp.itp, line 806]:
Duplicate atom index (25) in dihedrals
ERROR 75 [file gelatinitp.itp, line 806]:
No default Ryckaert-Bell. types
ERROR 76 [file gelatinitp.itp, line 855]:
No default Ryckaert-Bell. types
ERROR 77 [file gelatinitp.itp, line 861]:
No default Ryckaert-Bell. types
ERROR 78 [file gelatinitp.itp, line 862]:
No default Ryckaert-Bell. types
ERROR 79 [file gelatinitp.itp, line 863]:
No default Ryckaert-Bell. types
ERROR 80 [file gelatinitp.itp, line 864]:
No default Ryckaert-Bell. types
ERROR 81 [file gelatinitp.itp, line 867]:
No default Ryckaert-Bell. types
ERROR 82 [file gelatinitp.itp, line 868]:
No default Ryckaert-Bell. types
ERROR 83 [file gelatinitp.itp, line 869]:
No default Ryckaert-Bell. types
ERROR 84 [file gelatinitp.itp, line 870]:
No default Ryckaert-Bell. types
ERROR 85 [file gelatinitp.itp, line 871]:
No default Ryckaert-Bell. types
ERROR 86 [file gelatinitp.itp, line 884]:
No default Ryckaert-Bell. types
ERROR 87 [file gelatinitp.itp, line 886]:
No default Ryckaert-Bell. types
ERROR 88 [file gelatinitp.itp, line 888]:
No default Ryckaert-Bell. types
ERROR 89 [file gelatinitp.itp, line 890]:
No default Ryckaert-Bell. types
ERROR 90 [file gelatinitp.itp, line 891]:
No default Ryckaert-Bell. types
ERROR 91 [file gelatinitp.itp, line 892]:
No default Ryckaert-Bell. types
ERROR 92 [file gelatinitp.itp, line 911]:
No default Ryckaert-Bell. types
ERROR 93 [file gelatinitp.itp, line 912]:
No default Ryckaert-Bell. types
ERROR 94 [file gelatinitp.itp, line 913]:
No default Ryckaert-Bell. types
ERROR 95 [file gelatinitp.itp, line 917]:
No default Proper Dih. types
ERROR 96 [file gelatinitp.itp, line 918]:
No default Proper Dih. types
ERROR 97 [file gelatinitp.itp, line 919]:
No default Proper Dih. types
ERROR 98 [file gelatinitp.itp, line 920]:
No default Proper Dih. types
ERROR 99 [file gelatinitp.itp, line 921]:
No default Proper Dih. types
ERROR 100 [file gelatinitp.itp, line 922]:
No default Proper Dih. types
ERROR 101 [file gelatinitp.itp, line 923]:
No default Proper Dih. types
ERROR 102 [file gelatinitp.itp, line 924]:
No default Proper Dih. types
ERROR 103 [file gelatinitp.itp, line 925]:
No default Proper Dih. types
ERROR 104 [file gelatinitp.itp, line 926]:
No default Proper Dih. types
ERROR 105 [file gelatinitp.itp, line 927]:
No default Proper Dih. types
Excluding 3 bonded neighbours molecule type ‘GEL’
Excluding 2 bonded neighbours molecule type ‘SOL’
NOTE 2 [file topol.top, line 13]:
System has non-zero total charge: -4.450000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.
WARNING 1 [file topol.top, line 13]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a
physiological salt concentration.
It would be great if someone could point me towards the answer. Thank you