[gmx-users] 5. LINCS warning of QMMM simulation (andrian) (andrian)
Groenhof, Gerrit
ggroenh at gwdg.de
Thu Apr 28 10:12:18 CEST 2016
Hi,
Not sure if it was also you, but I recall replying not so long ago to a QM/MM question that all QM atoms must by inside the same topology (itp or top) for gromacs 4 and beyond. Splitting the QM atoms over multiple topologies leads to erroneous behaviour.
I don't know for sure if this is also the reason for the crahs, but considering that the some atoms are missing some forces it could be.
Best,
gerrit
Today's Topics:
1. Re: 5. LINCS warning of QMMM simulation (andrian) (andrian)
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
>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * 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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