[gmx-users] LINCS warning of QMMM simulation

andrian andrian.chem at gmail.com
Tue Apr 26 17:39:34 CEST 2016


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



More information about the gromacs.org_gmx-users mailing list