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

andrian andrian.chem at gmail.com
Wed Apr 27 01:11:33 CEST 2016


Hi,

thank you for your kindly reply...

system has been successfully minimized, restrained NVT/NPT equilibrated, 
and unrestrained Classical MM before... there is no problem..

*************************************************
here is my equilibrated structure (strarting configuration for qmmm)
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
**********************************************************
link atom is placed between C1 and C2 atoms, whereas its coordinate was 
calculated by x2 = [(0.153*x1)+ (0.153*x3)]/(0.153+0.153)..

do you have an idea ?

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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> End of gromacs.org_gmx-users Digest, Vol 144, Issue 151
> *******************************************************

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



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