[gmx-users] 5. LINCS warning of QMMM simulation (andrian)
Groenhof, Gerrit
ggroenh at gwdg.de
Tue Apr 26 20:48:53 CEST 2016
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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