[gmx-users] 5. LINCS warning of QMMM simulation (andrian)
andrian
andrian.chem at gmail.com
Wed Apr 27 17:06:55 CEST 2016
Hi,
anyone can help me ??? :(
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
>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 144, Issue 151
> *******************************************************
--
Andrian Saputra
Department of Pharmaceutical Science
Sumatera Institute of Technology, Indonesia
More information about the gromacs.org_gmx-users
mailing list