[gmx-users] 5. LINCS warning of QMMM simulation (andrian)
andrian
andrian.chem at gmail.com
Wed Apr 27 00:36:56 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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