Gromacs和orca交互 计算QM/MM ,生成tpr文件时出现问题



  • 想通过这两个软件计算分子激发态,首先通过amber软件生成了力场文件,在运用grompp命令生成tpr文件时会出现问题。
    使用5.0.7版本的时候,会提示This run will generate roughly 0 Mb of data double free or corruption (!prev)
    已放弃 (核心已转储)。
    在使用18.2版本的时候,有个错误 Invalid value for mdp option SAsteps. SAsteps should only consist of integers separated by spaces.不是SAsteps 就是 SAon 可这两个选项好像手册都没有教怎么设置。
    相应文件如下:
    TOP:
    ;
    ; File gromacs.top was generated
    ; By user: wang (1000)
    ; On host: wang
    ; At date: Fri. July 5 12:42:17 2018
    ;
    ; This is a standalone topology file
    ;
    ; Created by:
    ; ParmEd: convert.py, VERSION 3.0.0+57.g74a84d30
    ; Executable: convert.py
    ; Library dir: /usr/local/gromacs/share/gromacs/top
    ; Command line:
    ; convert.py

    [ defaults ]
    ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
    1 2 yes 0.5 0.83333333

    [ atomtypes ]
    ; name at.num mass charge ptype sigma epsilon
    o 8 16.000000 0.00000000 A 0.29599219 0.87864
    nh 7 14.010000 0.00000000 A 0.32499985 0.71128
    na 7 14.010000 0.00000000 A 0.32499985 0.71128
    c3 6 12.010000 0.00000000 A 0.33996695 0.4577296
    h1 1 1.008000 0.00000000 A 0.2471353 0.0656888
    ca 6 12.010000 0.00000000 A 0.33996695 0.359824
    ha 1 1.008000 0.00000000 A 0.25996425 0.06276
    cc 6 12.010000 0.00000000 A 0.33996695 0.359824
    c 6 12.010000 0.00000000 A 0.33996695 0.359824
    cd 6 12.010000 0.00000000 A 0.33996695 0.359824
    cf 6 12.010000 0.00000000 A 0.33996695 0.359824
    [ moleculetype ]
    ; Name nrexcl
    MOL 3
    [ atoms ]
    ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
    ; residue 1 MOL rtp MOL q 0.0
    1 o 1 MOL O 1 -0.47210000 16.000000 ; qtot -0.472100
    2 o 1 MOL O1 2 -0.48110000 16.000000 ; qtot -0.953200
    3 nh 1 MOL N 3 -0.66000000 14.010000 ; qtot -1.613200
    4 na 1 MOL N1 4 -0.08590000 14.010000 ; qtot -1.699100
    5 na 1 MOL N2 5 -0.08590000 14.010000 ; qtot -1.785000
    6 c3 1 MOL C 6 0.18860000 12.010000 ; qtot -1.596400
    7 h1 1 MOL H 7 0.03920000 1.008000 ; qtot -1.557200
    8 h1 1 MOL H1 8 0.03920000 1.008000 ; qtot -1.518000
    9 h1 1 MOL H2 9 0.03920000 1.008000 ; qtot -1.478800
    10 c3 1 MOL C1 10 0.18860000 12.010000 ; qtot -1.290200
    11 h1 1 MOL H3 11 0.03920000 1.008000 ; qtot -1.251000
    12 h1 1 MOL H4 12 0.03920000 1.008000 ; qtot -1.211800
    13 h1 1 MOL H5 13 0.03920000 1.008000 ; qtot -1.172600
    14 ca 1 MOL C2 14 0.18360000 12.010000 ; qtot -0.989000
    15 ca 1 MOL C3 15 -0.19950000 12.010000 ; qtot -1.188500
    16 ha 1 MOL H6 16 0.13550000 1.008000 ; qtot -1.053000
    17 ca 1 MOL C4 17 -0.06750000 12.010000 ; qtot -1.120500
    18 ha 1 MOL H7 18 0.14350000 1.008000 ; qtot -0.977000
    19 ca 1 MOL C5 19 -0.08780000 12.010000 ; qtot -1.064800
    20 ca 1 MOL C6 20 -0.06750000 12.010000 ; qtot -1.132300
    21 ha 1 MOL H8 21 0.14350000 1.008000 ; qtot -0.988800
    22 ca 1 MOL C7 22 -0.19950000 12.010000 ; qtot -1.188300
    23 ha 1 MOL H9 23 0.13550000 1.008000 ; qtot -1.052800
    24 cc 1 MOL C8 24 -0.11740000 12.010000 ; qtot -1.170200
    25 c 1 MOL C9 25 0.47030000 12.010000 ; qtot -0.699900
    26 c 1 MOL C10 26 0.46130000 12.010000 ; qtot -0.238600
    27 cd 1 MOL C11 27 -0.06620000 12.010000 ; qtot -0.304800
    28 cf 1 MOL C12 28 -0.26800000 12.010000 ; qtot -0.572800
    29 ha 1 MOL H10 29 0.15000000 1.008000 ; qtot -0.422800
    30 cc 1 MOL C13 30 0.11580000 12.010000 ; qtot -0.307000
    31 c3 1 MOL C14 31 0.00860000 12.010000 ; qtot -0.298400
    32 h1 1 MOL H11 32 0.05503300 1.008000 ; qtot -0.243367
    33 h1 1 MOL H12 33 0.05503300 1.008000 ; qtot -0.188334
    34 h1 1 MOL H13 34 0.05503300 1.008000 ; qtot -0.133301
    35 ca 1 MOL C15 35 -0.05620000 12.010000 ; qtot -0.189501
    36 ca 1 MOL C16 36 -0.11800000 12.010000 ; qtot -0.307501
    37 ha 1 MOL H14 37 0.14450000 1.008000 ; qtot -0.163001
    38 ca 1 MOL C17 38 -0.12700000 12.010000 ; qtot -0.290001
    39 ha 1 MOL H15 39 0.13750000 1.008000 ; qtot -0.152501
    40 ca 1 MOL C18 40 -0.12700000 12.010000 ; qtot -0.279501
    41 ha 1 MOL H16 41 0.13750000 1.008000 ; qtot -0.142001
    42 ca 1 MOL C19 42 -0.11800000 12.010000 ; qtot -0.260001
    43 ha 1 MOL H17 43 0.14450000 1.008000 ; qtot -0.115501
    44 ca 1 MOL C20 44 -0.05620000 12.010000 ; qtot -0.171701
    45 c3 1 MOL C21 45 0.00860000 12.010000 ; qtot -0.163101
    46 h1 1 MOL H18 46 0.05503300 1.008000 ; qtot -0.108068
    47 h1 1 MOL H19 47 0.05503300 1.008000 ; qtot -0.053035
    48 h1 1 MOL H20 48 0.05503300 1.008000 ; qtot 0.00000
    [ bonds ]
    ; ai aj funct c0 c1 c2 c3
    1 26 1 0.12183 533627.360000
    2 25 1 0.12183 533627.360000
    3 6 1 0.14640 273298.880000
    3 10 1 0.14640 273298.880000
    3 14 1 0.13859 349698.720000
    4 30 1 0.13802 356309.440000
    4 44 1 0.13840 351874.400000
    4 45 1 0.14629 274219.360000
    5 30 1 0.13802 356309.440000
    5 31 1 0.14629 274219.360000
    5 35 1 0.13840 351874.400000
    14 15 1 0.13984 385848.480000
    14 22 1 0.13984 385848.480000
    15 17 1 0.13984 385848.480000
    17 19 1 0.13984 385848.480000
    19 20 1 0.13984 385848.480000
    19 24 1 0.14555 322251.680000
    20 22 1 0.13984 385848.480000
    24 25 1 0.14676 310452.800000
    24 27 1 0.13729 419153.120000
    25 26 1 0.15482 244094.560000
    26 27 1 0.14676 310452.800000
    27 28 1 0.14540 323757.920000
    28 30 1 0.13656 429278.400000
    35 36 1 0.13984 385848.480000
    35 44 1 0.13984 385848.480000
    36 38 1 0.13984 385848.480000
    38 40 1 0.13984 385848.480000
    40 42 1 0.13984 385848.480000
    42 44 1 0.13984 385848.480000
    6 7 1 0.10969 276646.080000
    6 8 1 0.10969 276646.080000
    6 9 1 0.10969 276646.080000
    10 11 1 0.10969 276646.080000
    10 12 1 0.10969 276646.080000
    10 13 1 0.10969 276646.080000
    15 16 1 0.10860 289365.440000
    17 18 1 0.10860 289365.440000
    20 21 1 0.10860 289365.440000
    22 23 1 0.10860 289365.440000
    28 29 1 0.10883 286604.000000
    31 32 1 0.10969 276646.080000
    31 33 1 0.10969 276646.080000
    31 34 1 0.10969 276646.080000
    36 37 1 0.10860 289365.440000
    38 39 1 0.10860 289365.440000
    40 41 1 0.10860 289365.440000
    42 43 1 0.10860 289365.440000
    45 46 1 0.10969 276646.080000
    45 47 1 0.10969 276646.080000
    45 48 1 0.10969 276646.080000
    [ pairs ]
    ; ai aj funct c0 c1 c2 c3
    1 2 1
    1 24 1
    1 28 1
    2 19 1
    2 27 1
    3 17 1
    3 20 1
    4 31 1
    4 27 1
    4 36 1
    4 40 1
    5 45 1
    5 27 1
    5 38 1
    5 42 1
    6 15 1
    6 22 1
    10 15 1
    10 22 1
    14 19 1
    15 20 1
    15 24 1
    17 22 1
    17 25 1
    17 27 1
    19 26 1
    19 28 1
    20 25 1
    20 27 1
    22 24 1
    24 30 1
    25 28 1
    26 30 1
    28 44 1
    28 45 1
    28 31 1
    28 35 1
    30 42 1
    30 36 1
    31 36 1
    31 44 1
    35 40 1
    35 45 1
    36 42 1
    38 44 1
    42 45 1
    3 16 1
    3 23 1
    4 29 1
    4 43 1
    5 29 1
    5 37 1
    6 11 1
    6 12 1
    6 13 1
    7 10 1
    7 14 1
    8 10 1
    8 14 1
    9 10 1
    9 14 1
    11 14 1
    12 14 1
    13 14 1
    14 18 1
    14 21 1
    15 23 1
    16 22 1
    16 18 1
    16 19 1
    17 21 1
    18 20 1
    18 24 1
    19 23 1
    21 24 1
    21 23 1
    24 29 1
    26 29 1
    30 46 1
    30 47 1
    30 48 1
    30 32 1
    30 33 1
    30 34 1
    32 35 1
    33 35 1
    34 35 1
    35 39 1
    35 43 1
    36 41 1
    37 44 1
    37 39 1
    37 40 1
    38 43 1
    39 41 1
    39 42 1
    41 43 1
    41 44 1
    44 46 1
    44 47 1
    44 48 1

    [ angles ]
    ; ai aj ak funct c0 c1 c2 c3
    1 26 25 1 120.8500521 562.329600
    1 26 27 1 123.9300532 578.228800
    2 25 24 1 123.9300532 578.228800
    2 25 26 1 120.8500521 562.329600
    3 14 15 1 120.9500521 571.534400
    3 14 22 1 120.9500521 571.534400
    4 30 5 1 106.6000457 629.273600
    4 30 28 1 124.9300536 569.860800
    4 44 35 1 118.3400506 578.228800
    4 44 42 1 118.3400506 578.228800
    5 30 28 1 124.9300536 569.860800
    5 35 36 1 118.3400506 578.228800
    5 35 44 1 118.3400506 578.228800
    6 3 10 1 114.5100489 528.857600
    6 3 14 1 119.9800512 530.531200
    10 3 14 1 119.9800512 530.531200
    14 15 17 1 120.0200517 557.308800
    14 22 20 1 120.0200517 557.308800
    15 14 22 1 120.0200517 557.308800
    15 17 19 1 120.0200517 557.308800
    17 19 20 1 120.0200517 557.308800
    17 19 24 1 120.7900519 543.920000
    19 20 22 1 120.0200517 557.308800
    19 24 25 1 122.9500530 527.184000
    19 24 27 1 113.5100485 565.676800
    20 19 24 1 120.7900519 543.920000
    24 25 26 1 111.6700478 535.552000
    24 27 26 1 121.3500523 544.756800
    24 27 28 1 128.0500552 533.041600
    25 24 27 1 121.3500523 544.756800
    25 26 27 1 111.6700478 535.552000
    26 27 28 1 121.5700520 530.531200
    27 28 30 1 130.6100558 528.857600
    30 4 44 1 113.1500488 564.003200
    30 4 45 1 126.4600543 517.979200
    30 5 31 1 126.4600543 517.979200
    30 5 35 1 113.1500488 564.003200
    31 5 35 1 124.3600534 521.326400
    35 36 38 1 120.0200517 557.308800
    35 44 42 1 120.0200517 557.308800
    36 35 44 1 120.0200517 557.308800
    36 38 40 1 120.0200517 557.308800
    38 40 42 1 120.0200517 557.308800
    40 42 44 1 120.0200517 557.308800
    44 4 45 1 124.3600534 521.326400
    3 6 7 1 109.7900472 415.052800
    3 6 8 1 109.7900472 415.052800
    3 6 9 1 109.7900472 415.052800
    3 10 11 1 109.7900472 415.052800
    3 10 12 1 109.7900472 415.052800
    3 10 13 1 109.7900472 415.052800
    4 45 46 1 108.7800464 416.726400
    4 45 47 1 108.7800464 416.726400
    4 45 48 1 108.7800464 416.726400
    5 31 32 1 108.7800464 416.726400
    5 31 33 1 108.7800464 416.726400
    5 31 34 1 108.7800464 416.726400
    7 6 8 1 108.4600466 328.025600
    7 6 9 1 108.4600466 328.025600
    8 6 9 1 108.4600466 328.025600
    11 10 12 1 108.4600466 328.025600
    11 10 13 1 108.4600466 328.025600
    12 10 13 1 108.4600466 328.025600
    14 15 16 1 119.8800511 403.337600
    14 22 23 1 119.8800511 403.337600
    15 17 18 1 119.8800511 403.337600
    16 15 17 1 119.8800511 403.337600
    18 17 19 1 119.8800511 403.337600
    19 20 21 1 119.8800511 403.337600
    20 22 23 1 119.8800511 403.337600
    21 20 22 1 119.8800511 403.337600
    27 28 29 1 115.4400494 397.480000
    29 28 30 1 114.9500496 419.236800
    32 31 33 1 108.4600466 328.025600
    32 31 34 1 108.4600466 328.025600
    33 31 34 1 108.4600466 328.025600
    35 36 37 1 119.8800511 403.337600
    36 38 39 1 119.8800511 403.337600
    37 36 38 1 119.8800511 403.337600
    38 40 41 1 119.8800511 403.337600
    39 38 40 1 119.8800511 403.337600
    40 42 43 1 119.8800511 403.337600
    41 40 42 1 119.8800511 403.337600
    43 42 44 1 119.8800511 403.337600
    46 45 47 1 108.4600466 328.025600
    46 45 48 1 108.4600466 328.025600
    47 45 48 1 108.4600466 328.025600
    [ dihedrals ]
    ; ai aj ak al funct c0 c1 c2 c3 c4 c5
    1 26 25 2 1 180.0000771 1.2552000 2
    1 26 25 24 1 180.0000771 1.2552000 2
    1 26 27 24 1 180.0000771 12.0290000 2
    1 26 27 28 1 180.0000771 12.0290000 2
    2 25 24 19 1 180.0000771 12.0290000 2
    2 25 24 27 1 180.0000771 12.0290000 2
    2 25 26 27 1 180.0000771 1.2552000 2
    3 14 15 17 1 180.0000771 15.1670000 2
    3 14 22 20 1 180.0000771 15.1670000 2
    4 30 5 31 1 180.0000771 7.1128000 2
    4 30 5 35 1 180.0000771 7.1128000 2
    4 30 28 27 1 180.0000771 16.7360000 2
    4 44 35 5 1 180.0000771 15.1670000 2
    4 44 35 36 1 180.0000771 15.1670000 2
    4 44 42 40 1 180.0000771 15.1670000 2
    5 30 4 44 1 180.0000771 7.1128000 2
    5 30 4 45 1 180.0000771 7.1128000 2
    5 30 28 27 1 180.0000771 16.7360000 2
    5 35 36 38 1 180.0000771 15.1670000 2
    5 35 44 42 1 180.0000771 15.1670000 2
    6 3 14 15 1 180.0000771 4.3932000 2
    6 3 14 22 1 180.0000771 4.3932000 2
    10 3 14 15 1 180.0000771 4.3932000 2
    10 3 14 22 1 180.0000771 4.3932000 2
    14 15 17 19 1 180.0000771 15.1670000 2
    14 22 20 19 1 180.0000771 15.1670000 2
    15 14 22 20 1 180.0000771 15.1670000 2
    15 17 19 20 1 180.0000771 15.1670000 2
    15 17 19 24 1 180.0000771 15.1670000 2
    17 15 14 22 1 180.0000771 15.1670000 2
    17 19 20 22 1 180.0000771 15.1670000 2
    17 19 24 25 1 180.0000771 2.9288000 2
    17 19 24 27 1 180.0000771 2.9288000 2
    19 24 25 26 1 180.0000771 12.0290000 2
    19 24 27 26 1 180.0000771 16.7360000 2
    19 24 27 28 1 180.0000771 16.7360000 2
    20 19 24 25 1 180.0000771 2.9288000 2
    20 19 24 27 1 180.0000771 2.9288000 2
    22 20 19 24 1 180.0000771 15.1670000 2
    24 25 26 27 1 180.0000771 1.2552000 2
    24 27 26 25 1 180.0000771 12.0290000 2
    24 27 28 30 1 180.0000771 4.1840000 2
    25 24 27 26 1 180.0000771 16.7360000 2
    25 24 27 28 1 180.0000771 16.7360000 2
    25 26 27 28 1 180.0000771 12.0290000 2
    26 25 24 27 1 180.0000771 12.0290000 2
    26 27 28 30 1 180.0000771 4.1840000 2
    28 30 4 44 1 180.0000771 7.1128000 2
    28 30 4 45 1 180.0000771 7.1128000 2
    28 30 5 31 1 180.0000771 7.1128000 2
    28 30 5 35 1 180.0000771 7.1128000 2
    30 4 44 35 1 180.0000771 1.2552000 2
    30 4 44 42 1 180.0000771 1.2552000 2
    30 5 35 36 1 180.0000771 1.2552000 2
    30 5 35 44 1 180.0000771 1.2552000 2
    31 5 35 36 1 180.0000771 1.2552000 2
    31 5 35 44 1 180.0000771 1.2552000 2
    35 36 38 40 1 180.0000771 15.1670000 2
    35 44 4 45 1 180.0000771 1.2552000 2
    35 44 42 40 1 180.0000771 15.1670000 2
    36 35 44 42 1 180.0000771 15.1670000 2
    36 38 40 42 1 180.0000771 15.1670000 2
    38 36 35 44 1 180.0000771 15.1670000 2
    38 40 42 44 1 180.0000771 15.1670000 2
    42 44 4 45 1 180.0000771 1.2552000 2
    6 10 3 14 4 180.0000771 4.6024000 2
    45 44 4 30 4 180.0000771 4.6024000 2
    31 35 5 30 4 180.0000771 4.6024000 2
    15 22 14 3 4 180.0000771 4.6024000 2
    17 20 19 24 4 180.0000771 4.6024000 2
    25 19 24 27 4 180.0000771 4.6024000 2
    26 24 25 2 4 180.0000771 43.9320000 2
    1 26 27 25 4 180.0000771 43.9320000 2
    26 24 27 28 4 180.0000771 4.6024000 2
    28 4 30 5 4 180.0000771 4.6024000 2
    36 44 35 5 4 180.0000771 4.6024000 2
    35 42 44 4 4 180.0000771 4.6024000 2
    3 14 15 16 1 180.0000771 15.1670000 2
    3 14 22 23 1 180.0000771 15.1670000 2
    4 30 28 29 1 180.0000771 16.7360000 2
    4 44 42 43 1 180.0000771 15.1670000 2
    5 30 28 29 1 180.0000771 16.7360000 2
    5 35 36 37 1 180.0000771 15.1670000 2
    6 3 10 11 1 0.0000000 0.0000000 2
    6 3 10 12 1 0.0000000 0.0000000 2
    6 3 10 13 1 0.0000000 0.0000000 2
    7 6 3 10 1 0.0000000 0.0000000 2
    7 6 3 14 1 0.0000000 0.0000000 2
    8 6 3 10 1 0.0000000 0.0000000 2
    8 6 3 14 1 0.0000000 0.0000000 2
    9 6 3 10 1 0.0000000 0.0000000 2
    9 6 3 14 1 0.0000000 0.0000000 2
    11 10 3 14 1 0.0000000 0.0000000 2
    12 10 3 14 1 0.0000000 0.0000000 2
    13 10 3 14 1 0.0000000 0.0000000 2
    14 15 17 18 1 180.0000771 15.1670000 2
    14 22 20 21 1 180.0000771 15.1670000 2
    15 14 22 23 1 180.0000771 15.1670000 2
    16 15 14 22 1 180.0000771 15.1670000 2
    16 15 17 18 1 180.0000771 15.1670000 2
    16 15 17 19 1 180.0000771 15.1670000 2
    17 19 20 21 1 180.0000771 15.1670000 2
    18 17 19 20 1 180.0000771 15.1670000 2
    18 17 19 24 1 180.0000771 15.1670000 2
    19 20 22 23 1 180.0000771 15.1670000 2
    21 20 19 24 1 180.0000771 15.1670000 2
    21 20 22 23 1 180.0000771 15.1670000 2
    24 27 28 29 1 180.0000771 4.1840000 2
    26 27 28 29 1 180.0000771 4.1840000 2
    30 4 45 46 1 0.0000000 0.0000000 2
    30 4 45 47 1 0.0000000 0.0000000 2
    30 4 45 48 1 0.0000000 0.0000000 2
    30 5 31 32 1 0.0000000 0.0000000 2
    30 5 31 33 1 0.0000000 0.0000000 2
    30 5 31 34 1 0.0000000 0.0000000 2
    32 31 5 35 1 0.0000000 0.0000000 2
    33 31 5 35 1 0.0000000 0.0000000 2
    34 31 5 35 1 0.0000000 0.0000000 2
    35 36 38 39 1 180.0000771 15.1670000 2
    35 44 42 43 1 180.0000771 15.1670000 2
    36 38 40 41 1 180.0000771 15.1670000 2
    37 36 35 44 1 180.0000771 15.1670000 2
    37 36 38 39 1 180.0000771 15.1670000 2
    37 36 38 40 1 180.0000771 15.1670000 2
    38 40 42 43 1 180.0000771 15.1670000 2
    39 38 40 41 1 180.0000771 15.1670000 2
    39 38 40 42 1 180.0000771 15.1670000 2
    41 40 42 43 1 180.0000771 15.1670000 2
    41 40 42 44 1 180.0000771 15.1670000 2
    44 4 45 46 1 0.0000000 0.0000000 2
    44 4 45 47 1 0.0000000 0.0000000 2
    44 4 45 48 1 0.0000000 0.0000000 2
    14 17 15 16 4 180.0000771 4.6024000 2
    15 19 17 18 4 180.0000771 4.6024000 2
    19 22 20 21 4 180.0000771 4.6024000 2
    14 20 22 23 4 180.0000771 4.6024000 2
    30 27 28 29 4 180.0000771 4.6024000 2
    35 38 36 37 4 180.0000771 4.6024000 2
    36 40 38 39 4 180.0000771 4.6024000 2
    38 42 40 41 4 180.0000771 4.6024000 2
    40 44 42 43 4 180.0000771 4.6024000 2

    [ system ]
    ; Name
    Generic title
    [ molecules ]
    ; Compound #mols
    MOL 5
    mdp 文件:
    title = my_mdp_file
    cpp = /usr/bin/cpp -traditional
    include =
    define =
    integrator = md
    tinit = 0
    dt = 0.002
    nsteps = 500
    init_step = 0
    comm-mode = Linear
    nstcomm = 100
    comm_grps = system
    emtol = 10.0
    emstep = 0.0005
    nstxout = 10
    nstvout = 10
    nstfout = 10
    ; Checkpointing helps you continue after crashes
    nstcheckpoint = 10
    nstlog = 10
    nstenergy = 10
    nstxtcout = 10
    xtc-precision = 1000
    xtc_grps = MOL
    energygrps = QMatoms
    nstlist = 1
    cutoff-scheme =group
    ns_type = grid
    pbc = xyz
    rlist = 0.9
    domain-decomposition = no
    coulombtype = Cut-off
    rcoulomb-switch = 0
    rcoulomb = 0.9
    epsilon_r = 1
    epsilon_rf = 1
    vdwtype = Cut-Off
    rvdw-switch = 0
    rvdw = 0.9
    DispCorr = No
    fourierspacing = 0.12
    fourier_nx = 0
    fourier_ny = 0
    fourier_nz = 0
    pme_order = 4
    ewald_rtol = 1e-05
    ewald_geometry = 3d
    epsilon_surface = 0
    optimize_fft = no
    tcoupl = v-rescale
    tc-grps = MOL
    tau-t = 0.1
    ref-t = 300
    Pcoupl = Berendsen
    Pcoupltype = Isotropic
    tau-p = 1.0
    compressibility = 4.5e-5
    ref-p = 1.0
    gen_vel = no
    gen_temp = 00
    gen_seed = 18111976
    constraints = all-bonds
    constraint_algorithm = LINCS
    unconstrained_start = no
    Shake-SOR = no
    shake_tol = 0.0001
    lincs_order = 4
    lincs-iter = 1
    lincs_warnangle = 30
    morse = no
    QMMM = yes
    QMMM-grps = QMatoms
    QMmethod = B3LYP
    QMMMscheme = ONIOM
    QMbasis = 6-31G
    QMcharge = 0
    QMmult = 1
    ; CAS space options
    CASorbitals =
    CASelectrons =
    SAon =
    SAoff =
    SAsteps =

    请问应该怎么才能解决呢。



  • @shanguren 这些选项在gmx2016源码中的说明

    /* Surface hopping stuff */
        gmx_bool           bSH;     /* surface hopping (diabatic only)   */
        real               SAon;    /* at which energy gap the SA starts */
        real               SAoff;   /* at which energy gap the SA stops  */
        int                SAsteps; /* stepwise switchinng on the SA     */
        int                SAstep;  /* current state of SA               */
    

    如果你不需要的话, 就将它们删掉. 我不知道ORCA是如何处理的.


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