[gmx-users] 5. LINCS warning of QMMM simulation (andrian)

andrian andrian.chem at gmail.com
Wed Apr 27 14:05:21 CEST 2016


Hi Gerrit and all users,

do you have an idea about this problem ? now, i attached all my 
simulation files... hope someone can help.. thanks in advance


cheers


On 27/04/16 01:48, Groenhof, Gerrit wrote:
> Hi,
>
> Are you able to run a stable MM simulation with that system?
>
> Can you rule out that the system is not strained somewhere?
>
> Where do the starting coordinates come from?
>
> best,
>
> Gerrit
>
>
> Message: 5
> Date: Tue, 26 Apr 2016 22:39:22 +0700
> From: andrian <andrian.chem at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] LINCS warning of QMMM simulation
> Message-ID: <571F8BAA.30009 at gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear gromacs users
>
> i was trying to simulate simple QMMM of 2-chlorobutanol versus
> protonated water... my simulation was going well until LINCS warning
> appeared.
>
> "Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
> after LINCS: rms 0.133339, max 0.231421 (between atoms 2 and 6) bonds
> that rotated more than 30 degrees"
>
> i dont know whats the problem with the system or mdp setting...
>
> any kind of help is really appreciated... thank you
>
> cheers
>
> *************************
> here is my mdp file
> title                    = my_mdp_file
> cpp                      = /lib/cpp
> include                  =
> define                   =
>
> integrator               = md
> tinit                    = 0
> dt                       = 0.0005
> nsteps                   = 1000 ; 2ps
> nstcomm                  = 10
> comm_grps                = system
>
> nstxout                  = 10
> nstvout                  = 10
> nstfout                  = 10
> nstlog                   = 10
> nstenergy                = 10
> nstcalcenergy         = 10
> nstxtcout                = 10
> xtc_grps                 = system
> energygrps               = QMatoms MMatoms
>
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1
>
> coulombtype              = Reaction-Field
> rcoulomb                 = 1
> epsilon_r                = 1
> epsilon_rf         = 50
> vdwtype                  = cut-off
> rvdw                     = 1
> fourierspacing         = 0.12
> pme-order         = 4
> ewald-rtol         = 1e-5
> couple-intramol         = no
>
> tcoupl                   = v-rescale
> tc-grps                  = MMatoms QMatoms
> tau_t                    = 0.1 0  ; uncoupled QM atoms
> ref_t                    = 300 300
> pcoupl                   = Berendsen
> pcoupltype               = isotropic
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
>
> QMMM                     = yes
> QMMM-grps                = QMatoms
> QMmethod                 = RHF
> QMbasis                  = STO-3G
> QMMMscheme               = normal
> QMcharge                 = 1
> QMmult             = 1
>
> gen_vel                  = no
> gen_temp                 = 300
> gen_seed                 = 173529
>
> constraints              = all-bonds
> constraint_algorithm     = LINCS
> continuation         = no
> shake_sor         = no
> shake_tol                = 0.0005
> lincs_order              = 4
> lincs_iter         = 1
> lincs_warnangle          = 30
> morse                    = no
> *************************************************
>
> ***********************************************
> here is my topol.top
>
> ; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016
>
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> 1               2               yes             0.5     0.8333
>
> ; Include alkohol_GMX.itp topology
> #include "alkohol.acpype/alkohol_GMX.itp"
>
> ; Include Position restraint file
> #ifdef POSRES_ALKOHOL
> #include "posre_alkohol.itp"
> #endif
>
> #include "waterH.acpype/waterH_GMX.itp"
>
> ; Include Position restraint file
> #ifdef POSRES_WATER
> #include "posre_water.itp"
> #endif
>
> [ system ]
>    alkohol
>
> [ molecules ]
> ; Compound        nmols
> alkohol           1
> waterH          1
> ************************************
>
> *****************************************
> here is my alkohol itp file
>
> ; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016
>
> [ atomtypes ]
> ;name   bond_type at.num    mass     charge   ptype   sigma
> epsilon       Amb
>    c3       c3      6    0.00000  0.00000   A     3.39967e-01 4.57730e-01
> ; 1.91  0.1094
>    h1       h1      1    0.00000  0.00000   A     2.47135e-01 6.56888e-02
> ; 1.39  0.0157
>    oh       oh      8    0.00000  0.00000   A     3.06647e-01 8.80314e-01
> ; 1.72  0.2104
>    cl       cl     17    0.00000  0.00000   A     3.47094e-01 1.10876e+00
> ; 1.95  0.2650
>    hc       hc      1    0.00000  0.00000   A     2.64953e-01 6.56888e-02
> ; 1.49  0.0157
>    ho       ho      1    0.00000  0.00000   A     0.00000e+00 0.00000e+00
> ; 0.00  0.0000
>    LA      LA      1    0.00000  0.00000   A     0.000000+00 0.00000e+00
>
> [ moleculetype ]
> ;name            nrexcl
>    alkohol          3
>
> [ atoms ]
> ;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot
> bond_type
>        1   c3     1   UNL     C    1     0.122400     12.01000 ; qtot 0.122
>        2   c3     1   UNL    C1    2     0.015700     12.01000 ; qtot 0.138
>        3   h1     1   UNL     H    3     0.058200      1.00800 ; qtot 0.196
>        4   oh     1   UNL     O    4    -0.593801     16.00000 ; qtot -0.398
>        5   h1     1   UNL    H1    5     0.058200      1.00800 ; qtot -0.339
>        6   c3     1   UNL    C2    6    -0.083400     12.01000 ; qtot -0.423
>        7   h1     1   UNL    H2    7     0.086700      1.00800 ; qtot -0.336
>        8   cl     1   UNL    CL    8    -0.208400     35.45000 ; qtot -0.544
>        9   c3     1   UNL    C3    9    -0.097100     12.01000 ; qtot -0.642
>       10   hc     1   UNL    H3   10     0.053700      1.00800 ; qtot -0.588
>       11   hc     1   UNL    H4   11     0.053700      1.00800 ; qtot -0.534
>       12   hc     1   UNL    H5   12     0.041700      1.00800 ; qtot -0.492
>       13   hc     1   UNL    H6   13     0.041700      1.00800 ; qtot -0.451
>       14   hc     1   UNL    H7   14     0.041700      1.00800 ; qtot -0.409
>       15   ho     1   UNL    H8   15     0.409000      1.00800 ; qtot 0.000
>       16   LA     1   UNL    LA   16     0.000000      0.00000
>
> [ bonds ]
> ;   ai     aj funct   r             k
>        1      2   5   ; 1.5350e-01    2.5363e+05 ;      C - C1
>        1      3   5   ; 1.0930e-01    2.8108e+05 ;      C - H
>        1      4   5   ; 1.4260e-01    2.6284e+05 ;      C - O
>        1      5   5   ; 1.0930e-01    2.8108e+05 ;      C - H1
>        2      6   1    1.5350e-01    2.5363e+05 ;     C1 - C2
>        2      7   5   ; 1.0930e-01    2.8108e+05 ;     C1 - H2
>        2      8   5   ; 1.7860e-01    2.3347e+05 ;     C1 - CL
>        4     15   5   ; 9.7400e-02    3.0928e+05 ;      O - H8
>        6      9   1    1.5350e-01    2.5363e+05 ;     C2 - C3
>        6     10   1    1.0920e-01    2.8225e+05 ;     C2 - H3
>        6     11   1    1.0920e-01    2.8225e+05 ;     C2 - H4
>        9     12   1    1.0920e-01    2.8225e+05 ;     C3 - H5
>        9     13   1    1.0920e-01    2.8225e+05 ;     C3 - H6
>        9     14   1    1.0920e-01    2.8225e+05 ;     C3 - H7
>
> [ pairs ]
> ;   ai     aj    funct
>        1      9      1 ;      C - C3
>        1     10      1 ;      C - H3
>        1     11      1 ;      C - H4
>        2     12      1 ;     C1 - H5
>        2     13      1 ;     C1 - H6
>        2     14      1 ;     C1 - H7
>        2     15      1 ;     C1 - H8
>        3      6      1 ;      H - C2
>        3      7      1 ;      H - H2
>        3      8      1 ;      H - CL
>        3     15      1 ;      H - H8
>        4      6      1 ;      O - C2
>        4      7      1 ;      O - H2
>        4      8      1 ;      O - CL
>        5      6      1 ;     H1 - C2
>        5      7      1 ;     H1 - H2
>        5      8      1 ;     H1 - CL
>        5     15      1 ;     H1 - H8
>        7      9      1 ;     H2 - C3
>        7     10      1 ;     H2 - H3
>        7     11      1 ;     H2 - H4
>        8      9      1 ;     CL - C3
>        8     10      1 ;     CL - H3
>        8     11      1 ;     CL - H4
>       10     12      1 ;     H3 - H5
>       10     13      1 ;     H3 - H6
>       10     14      1 ;     H3 - H7
>       11     12      1 ;     H4 - H5
>       11     13      1 ;     H4 - H6
>       11     14      1 ;     H4 - H7
>
> [ angles ]
> ;   ai     aj     ak    funct   theta         cth
>        1      2      6      1    1.1063e+02    5.2894e+02 ;      C -
> C1     - C2
>        1      2      7      1    1.1007e+02    3.8794e+02 ;      C -
> C1     - H2
>        1      2      8      1    1.1033e+02    4.8409e+02 ;      C -
> C1     - CL
>        1      4     15      1    1.0816e+02    3.9405e+02 ;      C -
> O      - H8
>        2      1      3      1    1.1007e+02    3.8794e+02 ;     C1 -
> C      - H
>        2      1      4      1    1.0943e+02    5.6668e+02 ;     C1 -
> C      - O
>        2      1      5      1    1.1007e+02    3.8794e+02 ;     C1 -
> C      - H1
>        2      6      9      1    1.1063e+02    5.2894e+02 ;     C1 -
> C2     - C3
>        2      6     10      1    1.1005e+02    3.8802e+02 ;     C1 -
> C2     - H3
>        2      6     11      1    1.1005e+02    3.8802e+02 ;     C1 -
> C2     - H4
>        3      1      4      1    1.0988e+02    4.2652e+02 ;      H -
> C      - O
>        3      1      5      1    1.0955e+02    3.2786e+02 ;      H -
> C      - H1
>        4      1      5      1    1.0988e+02    4.2652e+02 ;      O -
> C      - H1
>        6      2      7      1    1.1007e+02    3.8794e+02 ;     C2 -
> C1     - H2
>        6      2      8      1    1.1033e+02    4.8409e+02 ;     C2 -
> C1     - CL
>        6      9     12      1    1.1005e+02    3.8802e+02 ;     C2 -
> C3     - H5
>        6      9     13      1    1.1005e+02    3.8802e+02 ;     C2 -
> C3     - H6
>        6      9     14      1    1.1005e+02    3.8802e+02 ;     C2 -
> C3     - H7
>        7      2      8      1    1.0593e+02    3.4024e+02 ;     H2 -
> C1     - CL
>        9      6     10      1    1.1005e+02    3.8802e+02 ;     C3 -
> C2     - H3
>        9      6     11      1    1.1005e+02    3.8802e+02 ;     C3 -
> C2     - H4
>       10      6     11      1    1.0835e+02    3.2995e+02 ;     H3 -
> C2     - H4
>       12      9     13      1    1.0835e+02    3.2995e+02 ;     H5 -
> C3     - H6
>       12      9     14      1    1.0835e+02    3.2995e+02 ;     H5 -
> C3     - H7
>       13      9     14      1    1.0835e+02    3.2995e+02 ;     H6 -
> C3     - H7
>
> [ dihedrals ] ; propers
> ; treated as RBs in GROMACS to use combine multiple AMBER torsions per
> quartet
> ;    i      j      k      l   func    C0         C1 C2
> C3         C4         C5
>        1      2      6      9      3    3.68192    3.09616 -2.09200
> -3.01248    0.00000    0.00000 ;      C-    C1-    C2- C3
>        1      2      6     10      3    0.66944    2.00832 0.00000
> -2.67776    0.00000    0.00000 ;      C-    C1-    C2- H3
>        1      2      6     11      3    0.66944    2.00832 0.00000
> -2.67776    0.00000    0.00000 ;      C-    C1-    C2- H4
>        2      1      4     15      3    1.71544    0.96232 0.00000
> -2.67776    0.00000    0.00000 ;     C1-     C-     O- H8
>        2      6      9     12      3    0.66944    2.00832 0.00000
> -2.67776    0.00000    0.00000 ;     C1-    C2-    C3- H5
>        2      6      9     13      3    0.66944    2.00832 0.00000
> -2.67776    0.00000    0.00000 ;     C1-    C2-    C3- H6
>        2      6      9     14      3    0.66944    2.00832 0.00000
> -2.67776    0.00000    0.00000 ;     C1-    C2-    C3- H7
>        3      1      2      6      3    0.65084    1.95253 0.00000
> -2.60338    0.00000    0.00000 ;      H-     C-    C1- C2
>        3      1      2      7      3    0.65084    1.95253 0.00000
> -2.60338    0.00000    0.00000 ;      H-     C-    C1- H2
>        3      1      2      8      3    1.04600   -1.04600 0.00000
> 0.00000    0.00000    0.00000 ;      H-     C-    C1- CL
>        3      1      4     15      3    0.69733    2.09200 0.00000
> -2.78933    0.00000    0.00000 ;      H-     C-     O- H8
>        4      1      2      6      3    0.65084    1.95253 0.00000
> -2.60338    0.00000    0.00000 ;      O-     C-    C1- C2
>        4      1      2      7      3    1.04600   -1.04600 0.00000
> 0.00000    0.00000    0.00000 ;      O-     C-    C1- H2
>        4      1      2      8      3    0.65084    1.95253 0.00000
> -2.60338    0.00000    0.00000 ;      O-     C-    C1- CL
>        5      1      2      6      3    0.65084    1.95253 0.00000
> -2.60338    0.00000    0.00000 ;     H1-     C-    C1- C2
>        5      1      2      7      3    0.65084    1.95253 0.00000
> -2.60338    0.00000    0.00000 ;     H1-     C-    C1- H2
>        5      1      2      8      3    1.04600   -1.04600 0.00000
> 0.00000    0.00000    0.00000 ;     H1-     C-    C1- CL
>        5      1      4     15      3    0.69733    2.09200 0.00000
> -2.78933    0.00000    0.00000 ;     H1-     C-     O- H8
>        7      2      6      9      3    0.65084    1.95253 0.00000
> -2.60338    0.00000    0.00000 ;     H2-    C1-    C2- C3
>        7      2      6     10      3    0.65084    1.95253 0.00000
> -2.60338    0.00000    0.00000 ;     H2-    C1-    C2- H3
>        7      2      6     11      3    0.65084    1.95253 0.00000
> -2.60338    0.00000    0.00000 ;     H2-    C1-    C2- H4
>        8      2      6      9      3    0.65084    1.95253 0.00000
> -2.60338    0.00000    0.00000 ;     CL-    C1-    C2- C3
>        8      2      6     10      3    1.04600   -1.04600 0.00000
> 0.00000    0.00000    0.00000 ;     CL-    C1-    C2- H3
>        8      2      6     11      3    1.04600   -1.04600 0.00000
> 0.00000    0.00000    0.00000 ;     CL-    C1-    C2- H4
>       10      6      9     12      3    0.62760    1.88280 0.00000
> -2.51040    0.00000    0.00000 ;     H3-    C2-    C3- H5
>       10      6      9     13      3    0.62760    1.88280 0.00000
> -2.51040    0.00000    0.00000 ;     H3-    C2-    C3- H6
>       10      6      9     14      3    0.62760    1.88280 0.00000
> -2.51040    0.00000    0.00000 ;     H3-    C2-    C3- H7
>       11      6      9     12      3    0.62760    1.88280 0.00000
> -2.51040    0.00000    0.00000 ;     H4-    C2-    C3- H5
>       11      6      9     13      3    0.62760    1.88280 0.00000
> -2.51040    0.00000    0.00000 ;     H4-    C2-    C3- H6
>       11      6      9     14      3    0.62760    1.88280 0.00000
> -2.51040    0.00000    0.00000 ;     H4-    C2-    C3- H7
>
> [ virtual_sites2 ]
> 16 2 6 1 0.65
>
> [ constraints ]
> 2 6 2 0.153
> **************************************************************************************************************
> here is my protonated water itp file
> ; waterH_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:17 2016
>
> [ moleculetype ]
> ;name            nrexcl
>    waterH           3
>
> [ atoms ]
> ;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot
> bond_type
>        1   oh     1   HOH     O    1    -0.710002     16.00000 ; qtot -0.710
>        2   ho     1   HOH     H    2     0.570001      1.00800 ; qtot -0.140
>        3   ho     1   HOH    H1    3     0.570001      1.00800 ; qtot 0.430
>        4   ho     1   HOH    H2    4     0.570001      1.00800 ; qtot 1.000
>
> [ bonds ]
> ;   ai     aj funct   r             k
>        1      2   5  ;  9.7400e-02    3.0928e+05 ;      O - H
>        1      3   5  ;  9.7400e-02    3.0928e+05 ;      O - H1
>        1      4   5  ;  9.7400e-02    3.0928e+05 ;      O - H2
>
> [ angles ]
> ;   ai     aj     ak    funct   theta         cth
>        2      1      3      1    1.0480e+02    3.5087e+02 ;      H -
> O      - H1
>        2      1      4      1    1.0480e+02    3.5087e+02 ;      H -
> O      - H2
>        3      1      4      1    1.0480e+02    3.5087e+02 ;     H1 -
> O      - H2
> *************************************************************************
>
> **********************************************************************
> here is my ORCAINFO file
> ! AM1 OPT tightSCF
> ! PModel                 # Initial density Guess
> ! XYZFile                # Type of Coordinates
>
> %scf
>     SCFMode Direct
>     MaxIter 1500
>     UseCheapInts true
> end
> **************************************************
>
>
>
> --
> Andrian Saputra
> Department of Pharmaceutical Science
> Sumatera Institute of Technology, Indonesia
>
>
>
> ------------------------------
>
> --
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>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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>
> End of gromacs.org_gmx-users Digest, Vol 144, Issue 151
> *******************************************************

-- 
Andrian Saputra
Department of Pharmaceutical Science
Sumatera Institute of Technology, Indonesia

-------------- next part --------------
; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ atomtypes ]
;name   bond_type at.num    mass     charge   ptype   sigma         epsilon       Amb
 c3       c3      6    0.00000  0.00000   A     3.39967e-01   4.57730e-01 ; 1.91  0.1094
 h1       h1      1    0.00000  0.00000   A     2.47135e-01   6.56888e-02 ; 1.39  0.0157
 oh       oh      8    0.00000  0.00000   A     3.06647e-01   8.80314e-01 ; 1.72  0.2104
 cl       cl     17    0.00000  0.00000   A     3.47094e-01   1.10876e+00 ; 1.95  0.2650
 hc       hc      1    0.00000  0.00000   A     2.64953e-01   6.56888e-02 ; 1.49  0.0157
 ho       ho      1    0.00000  0.00000   A     0.00000e+00   0.00000e+00 ; 0.00  0.0000
 LA	  LA	  1    0.00000  0.00000   A     0.000000+00   0.00000e+00

[ moleculetype ]
;name            nrexcl
 alkohol          3

[ atoms ]
;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot   bond_type
     1   c3     1   UNL     C    1     0.122400     12.01000 ; qtot 0.122
     2   c3     1   UNL    C1    2     0.015700     12.01000 ; qtot 0.138
     3   h1     1   UNL     H    3     0.058200      1.00800 ; qtot 0.196
     4   oh     1   UNL     O    4    -0.593801     16.00000 ; qtot -0.398
     5   h1     1   UNL    H1    5     0.058200      1.00800 ; qtot -0.339
     6   c3     1   UNL    C2    6    -0.083400     12.01000 ; qtot -0.423
     7   h1     1   UNL    H2    7     0.086700      1.00800 ; qtot -0.336
     8   cl     1   UNL    CL    8    -0.208400     35.45000 ; qtot -0.544
     9   c3     1   UNL    C3    9    -0.097100     12.01000 ; qtot -0.642
    10   hc     1   UNL    H3   10     0.053700      1.00800 ; qtot -0.588
    11   hc     1   UNL    H4   11     0.053700      1.00800 ; qtot -0.534
    12   hc     1   UNL    H5   12     0.041700      1.00800 ; qtot -0.492
    13   hc     1   UNL    H6   13     0.041700      1.00800 ; qtot -0.451
    14   hc     1   UNL    H7   14     0.041700      1.00800 ; qtot -0.409
    15   ho     1   UNL    H8   15     0.409000      1.00800 ; qtot 0.000
    16   LA     1   UNL    LA   16     0.000000      0.00000

[ bonds ]
;   ai     aj funct   r             k
     1      2   5   ; 1.5350e-01    2.5363e+05 ;      C - C1    
     1      3   5   ; 1.0930e-01    2.8108e+05 ;      C - H     
     1      4   5   ; 1.4260e-01    2.6284e+05 ;      C - O     
     1      5   5   ; 1.0930e-01    2.8108e+05 ;      C - H1    
     2      6   1    1.5350e-01    2.5363e+05 ;     C1 - C2    
     2      7   5   ; 1.0930e-01    2.8108e+05 ;     C1 - H2    
     2      8   5   ; 1.7860e-01    2.3347e+05 ;     C1 - CL    
     4     15   5   ; 9.7400e-02    3.0928e+05 ;      O - H8    
     6      9   1    1.5350e-01    2.5363e+05 ;     C2 - C3    
     6     10   1    1.0920e-01    2.8225e+05 ;     C2 - H3    
     6     11   1    1.0920e-01    2.8225e+05 ;     C2 - H4    
     9     12   1    1.0920e-01    2.8225e+05 ;     C3 - H5    
     9     13   1    1.0920e-01    2.8225e+05 ;     C3 - H6    
     9     14   1    1.0920e-01    2.8225e+05 ;     C3 - H7    

[ pairs ]
;   ai     aj    funct
     1      9      1 ;      C - C3    
     1     10      1 ;      C - H3    
     1     11      1 ;      C - H4    
     2     12      1 ;     C1 - H5    
     2     13      1 ;     C1 - H6    
     2     14      1 ;     C1 - H7    
     2     15      1 ;     C1 - H8    
     3      6      1 ;      H - C2    
     3      7      1 ;      H - H2    
     3      8      1 ;      H - CL    
     3     15      1 ;      H - H8    
     4      6      1 ;      O - C2    
     4      7      1 ;      O - H2    
     4      8      1 ;      O - CL    
     5      6      1 ;     H1 - C2    
     5      7      1 ;     H1 - H2    
     5      8      1 ;     H1 - CL    
     5     15      1 ;     H1 - H8    
     7      9      1 ;     H2 - C3    
     7     10      1 ;     H2 - H3    
     7     11      1 ;     H2 - H4    
     8      9      1 ;     CL - C3    
     8     10      1 ;     CL - H3    
     8     11      1 ;     CL - H4    
    10     12      1 ;     H3 - H5    
    10     13      1 ;     H3 - H6    
    10     14      1 ;     H3 - H7    
    11     12      1 ;     H4 - H5    
    11     13      1 ;     H4 - H6    
    11     14      1 ;     H4 - H7    

[ angles ]
;   ai     aj     ak    funct   theta         cth
     1      2      6      1    1.1063e+02    5.2894e+02 ;      C - C1     - C2    
     1      2      7      1    1.1007e+02    3.8794e+02 ;      C - C1     - H2    
     1      2      8      1    1.1033e+02    4.8409e+02 ;      C - C1     - CL    
     1      4     15      1    1.0816e+02    3.9405e+02 ;      C - O      - H8    
     2      1      3      1    1.1007e+02    3.8794e+02 ;     C1 - C      - H     
     2      1      4      1    1.0943e+02    5.6668e+02 ;     C1 - C      - O     
     2      1      5      1    1.1007e+02    3.8794e+02 ;     C1 - C      - H1    
     2      6      9      1    1.1063e+02    5.2894e+02 ;     C1 - C2     - C3    
     2      6     10      1    1.1005e+02    3.8802e+02 ;     C1 - C2     - H3    
     2      6     11      1    1.1005e+02    3.8802e+02 ;     C1 - C2     - H4    
     3      1      4      1    1.0988e+02    4.2652e+02 ;      H - C      - O     
     3      1      5      1    1.0955e+02    3.2786e+02 ;      H - C      - H1    
     4      1      5      1    1.0988e+02    4.2652e+02 ;      O - C      - H1    
     6      2      7      1    1.1007e+02    3.8794e+02 ;     C2 - C1     - H2    
     6      2      8      1    1.1033e+02    4.8409e+02 ;     C2 - C1     - CL    
     6      9     12      1    1.1005e+02    3.8802e+02 ;     C2 - C3     - H5    
     6      9     13      1    1.1005e+02    3.8802e+02 ;     C2 - C3     - H6    
     6      9     14      1    1.1005e+02    3.8802e+02 ;     C2 - C3     - H7    
     7      2      8      1    1.0593e+02    3.4024e+02 ;     H2 - C1     - CL    
     9      6     10      1    1.1005e+02    3.8802e+02 ;     C3 - C2     - H3    
     9      6     11      1    1.1005e+02    3.8802e+02 ;     C3 - C2     - H4    
    10      6     11      1    1.0835e+02    3.2995e+02 ;     H3 - C2     - H4    
    12      9     13      1    1.0835e+02    3.2995e+02 ;     H5 - C3     - H6    
    12      9     14      1    1.0835e+02    3.2995e+02 ;     H5 - C3     - H7    
    13      9     14      1    1.0835e+02    3.2995e+02 ;     H6 - C3     - H7    

[ dihedrals ] ; propers
; treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet
;    i      j      k      l   func    C0         C1         C2         C3         C4         C5
     1      2      6      9      3    3.68192    3.09616   -2.09200   -3.01248    0.00000    0.00000 ;      C-    C1-    C2-    C3
     1      2      6     10      3    0.66944    2.00832    0.00000   -2.67776    0.00000    0.00000 ;      C-    C1-    C2-    H3
     1      2      6     11      3    0.66944    2.00832    0.00000   -2.67776    0.00000    0.00000 ;      C-    C1-    C2-    H4
     2      1      4     15      3    1.71544    0.96232    0.00000   -2.67776    0.00000    0.00000 ;     C1-     C-     O-    H8
     2      6      9     12      3    0.66944    2.00832    0.00000   -2.67776    0.00000    0.00000 ;     C1-    C2-    C3-    H5
     2      6      9     13      3    0.66944    2.00832    0.00000   -2.67776    0.00000    0.00000 ;     C1-    C2-    C3-    H6
     2      6      9     14      3    0.66944    2.00832    0.00000   -2.67776    0.00000    0.00000 ;     C1-    C2-    C3-    H7
     3      1      2      6      3    0.65084    1.95253    0.00000   -2.60338    0.00000    0.00000 ;      H-     C-    C1-    C2
     3      1      2      7      3    0.65084    1.95253    0.00000   -2.60338    0.00000    0.00000 ;      H-     C-    C1-    H2
     3      1      2      8      3    1.04600   -1.04600    0.00000    0.00000    0.00000    0.00000 ;      H-     C-    C1-    CL
     3      1      4     15      3    0.69733    2.09200    0.00000   -2.78933    0.00000    0.00000 ;      H-     C-     O-    H8
     4      1      2      6      3    0.65084    1.95253    0.00000   -2.60338    0.00000    0.00000 ;      O-     C-    C1-    C2
     4      1      2      7      3    1.04600   -1.04600    0.00000    0.00000    0.00000    0.00000 ;      O-     C-    C1-    H2
     4      1      2      8      3    0.65084    1.95253    0.00000   -2.60338    0.00000    0.00000 ;      O-     C-    C1-    CL
     5      1      2      6      3    0.65084    1.95253    0.00000   -2.60338    0.00000    0.00000 ;     H1-     C-    C1-    C2
     5      1      2      7      3    0.65084    1.95253    0.00000   -2.60338    0.00000    0.00000 ;     H1-     C-    C1-    H2
     5      1      2      8      3    1.04600   -1.04600    0.00000    0.00000    0.00000    0.00000 ;     H1-     C-    C1-    CL
     5      1      4     15      3    0.69733    2.09200    0.00000   -2.78933    0.00000    0.00000 ;     H1-     C-     O-    H8
     7      2      6      9      3    0.65084    1.95253    0.00000   -2.60338    0.00000    0.00000 ;     H2-    C1-    C2-    C3
     7      2      6     10      3    0.65084    1.95253    0.00000   -2.60338    0.00000    0.00000 ;     H2-    C1-    C2-    H3
     7      2      6     11      3    0.65084    1.95253    0.00000   -2.60338    0.00000    0.00000 ;     H2-    C1-    C2-    H4
     8      2      6      9      3    0.65084    1.95253    0.00000   -2.60338    0.00000    0.00000 ;     CL-    C1-    C2-    C3
     8      2      6     10      3    1.04600   -1.04600    0.00000    0.00000    0.00000    0.00000 ;     CL-    C1-    C2-    H3
     8      2      6     11      3    1.04600   -1.04600    0.00000    0.00000    0.00000    0.00000 ;     CL-    C1-    C2-    H4
    10      6      9     12      3    0.62760    1.88280    0.00000   -2.51040    0.00000    0.00000 ;     H3-    C2-    C3-    H5
    10      6      9     13      3    0.62760    1.88280    0.00000   -2.51040    0.00000    0.00000 ;     H3-    C2-    C3-    H6
    10      6      9     14      3    0.62760    1.88280    0.00000   -2.51040    0.00000    0.00000 ;     H3-    C2-    C3-    H7
    11      6      9     12      3    0.62760    1.88280    0.00000   -2.51040    0.00000    0.00000 ;     H4-    C2-    C3-    H5
    11      6      9     13      3    0.62760    1.88280    0.00000   -2.51040    0.00000    0.00000 ;     H4-    C2-    C3-    H6
    11      6      9     14      3    0.62760    1.88280    0.00000   -2.51040    0.00000    0.00000 ;     H4-    C2-    C3-    H7

[ virtual_sites2 ]
16 2 6 1 0.65

[ constraints ]
2 6 2 0.153
-------------- next part --------------
; waterH_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:17 2016

[ moleculetype ]
;name            nrexcl
 waterH           3

[ atoms ]
;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot   bond_type
     1   oh     1   HOH     O    1    -0.710002     16.00000 ; qtot -0.710
     2   ho     1   HOH     H    2     0.570001      1.00800 ; qtot -0.140
     3   ho     1   HOH    H1    3     0.570001      1.00800 ; qtot 0.430
     4   ho     1   HOH    H2    4     0.570001      1.00800 ; qtot 1.000

[ bonds ]
;   ai     aj funct   r             k
     1      2   5  ;  9.7400e-02    3.0928e+05 ;      O - H     
     1      3   5  ;  9.7400e-02    3.0928e+05 ;      O - H1    
     1      4   5  ;  9.7400e-02    3.0928e+05 ;      O - H2    

[ angles ]
;   ai     aj     ak    funct   theta         cth
     2      1      3      1    1.0480e+02    3.5087e+02 ;      H - O      - H1    
     2      1      4      1    1.0480e+02    3.5087e+02 ;      H - O      - H2    
     3      1      4      1    1.0480e+02    3.5087e+02 ;     H1 - O      - H2    
-------------- next part --------------
Grunge ROck MAChoS
   20
    1UNL      C    1   2.600   2.380   2.439
    1UNL     C1    2   2.540   2.521   2.421
    1UNL      H    3   2.554   2.304   2.376
    1UNL      O    4   2.587   2.339   2.575
    1UNL     H1    5   2.708   2.376   2.422
    1UNL     C2    6   2.388   2.522   2.440
    1UNL     H2    7   2.554   2.559   2.319
    1UNL     CL    8   2.612   2.651   2.519
    1UNL     C3    9   2.327   2.649   2.379
    1UNL     H3   10   2.363   2.497   2.543
    1UNL     H4   11   2.354   2.441   2.375
    1UNL     H5   12   2.287   2.725   2.447
    1UNL     H6   13   2.241   2.628   2.315
    1UNL     H7   14   2.400   2.708   2.323
    1UNL     H8   15   2.565   2.244   2.568
    1UNL     LA   16   2.464   2.521   2.430
    2HOH      O   17   2.592   2.475   2.796
    2HOH      H   18   2.684   2.494   2.769
    2HOH     H1   19   2.589   2.419   2.716
    2HOH     H2   20   2.560   2.560   2.760
   5.00000   5.00000   5.00000
-------------- next part --------------
; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               2               yes             0.5     0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include "waterH.acpype/waterH_GMX.itp"

; Include Position restraint file
#ifdef POSRES_WATER
#include "posre_water.itp"
#endif

[ system ]
 alkohol

[ molecules ]
; Compound        nmols
alkohol           1     
waterH		  1
-------------- next part --------------
[ System ]
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15 
  16   17   18   19   20 
[ Other ]
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15 
  16 
[ UNL ]
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15 
  16 
[ Water ]
  17   18   19   20 
[ SOL ]
  17   18   19   20 
[ non-Water ]
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15 
  16 
[ QMatoms ]
   1    2    3    4    5    7    8   15   16   17   18   19   20 
[ MMatoms ]
   6    9   10   11   12   13   14 
-------------- next part --------------
! AM1 OPT tightSCF
! PModel                 # Initial density Guess
! XYZFile                # Type of Coordinates

%scf
  SCFMode Direct
  MaxIter 1500
  UseCheapInts true
end
-------------- next part --------------
title                    = my_mdp_file
cpp                      = /lib/cpp
include                  =
define                   = 

integrator               = md
tinit                    = 0
dt                       = 0.0005
nsteps                   = 1000 ; 2ps
nstcomm                  = 10
comm_grps                = system

nstxout                  = 10
nstvout                  = 10
nstfout                  = 10
nstlog                   = 10
nstenergy                = 10
nstcalcenergy		 = 10
nstxtcout                = 10
xtc_grps                 = system
energygrps               = QMatoms MMatoms

nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1

coulombtype              = Reaction-Field
rcoulomb                 = 1
epsilon_r                = 1
epsilon_rf		 = 50
vdwtype                  = cut-off
rvdw                     = 1
fourierspacing		 = 0.12
pme-order		 = 4
ewald-rtol		 = 1e-5
couple-intramol		 = no

tcoupl                   = v-rescale
tc-grps                  = MMatoms QMatoms
tau_t                    = 0.1 0  ; QM atoms are uncoupled
ref_t                    = 300 300
pcoupl                   = Berendsen
pcoupltype               = isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0

QMMM                     = yes
QMMM-grps                = QMatoms
QMmethod                 = RHF
QMbasis                  = STO-3G
QMMMscheme               = ONIOM
QMcharge                 = 1
QMmult			 = 1

gen_vel                  = no
gen_temp                 = 300
gen_seed                 = 173529

constraints              = all-bonds
constraint_algorithm     = LINCS
continuation		 = no
shake_sor		 = no
shake_tol                = 0.0005
lincs_order              = 4
lincs_iter		 = 1
lincs_warnangle          = 30
morse                    = no


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