[gmx-users] using the Fourier function for dihedral in the OPLS FF
Saeed Nasiri
s.t.nasiri at gmail.com
Sat Jun 3 10:53:51 CEST 2017
Dear Justin
I changed the directives to [ dihedraltypes ] in the dihedral.itp file and
it seem OK. However, there are other problems. First, I can't run any
simulation is vacuum, because the grompp says that the box is small. I use
a really big box for test (9208.29 (nm^3)) with this command:
gmx_mpi_d editconf -f BMIM_pro.gro -o BMIM_box.gro -c -d 10.0 -bt cubic
***************************************************************************************
.....
NOTE 1 [file minim.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to 675038336
Generated 340725 of the 340725 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 340725 of the 340725 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'IL_cat_chain_A'
ERROR 1 [file topol.top, line 274]:
ERROR: The cut-off length is longer than half the shortest box vector or
longer than the smallest box diagonal element. Increase the box size or
decrease rlist.
Removing all charge groups because cutoff-scheme=Verlet
There was 1 note
-------------------------------------------------------
Program gmx grompp, VERSION 5.1.4
Source code file:
/home/nasiri/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line: 1738
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Halting program gmx grompp
**************************************************************************************************
Then I add water to the box (the smaller box 9208.29nm^3 ) without any
problem and I run the energy minimization. Unfortunately, the structure of
the molecule is destroyed again !!!
I don't know what is the problem. The changed parts of the OPLS FF files
are shown in follows. Please tell me what should I do ?
Thanks so much.
**********************dihedral.itp**************************************
[ dihedraltypes ]
; i j k l type v1 v2 v3 v4
; Br C CB CTT 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ; acyl halide
HCC CTT CSS HCC 5 0.00000 0.00000 1.33050 0.00000
HCC CSS C22 HCC 5 0.00000 0.00000 1.33050 0.00000
HCC C22 C11 H11 5 0.00000 0.00000 1.33050 0.00000
CTT CSS C22 HCC 5 0.00000 0.00000 1.53130 0.00000
CSS C22 C11 H11 5 0.00000 0.00000 1.53130 0.00000
C11 C22 CSS HCC 5 0.00000 0.00000 1.53130 0.00000
C22 CSS CTT HCC 5 0.00000 0.00000 1.53130 0.00000
CTT CSS C22 C11 5 7.28000 -0.65690 1.16730
0.00000
CWW NAA CRR NAA 5 0.00000 19.46000 0.00000
0.00000
CWW NAA CRR HCR 5 0.00000 19.46000 0.00000
0.00000
C11 NAA CRR NAA 5 0.00000 19.46000 0.00000
0.00000
C11 NAA CRR HCR 5 0.00000 19.46000 0.00000
0.00000
CRR NAA CWW CWW 5 0.00000 12.55000 0.00000
0.00000
CRR NAA CWW HCW 5 0.00000 12.55000 0.00000
0.00000
C11 NAA CWW CWW 5 0.00000 12.55000 0.00000
0.00000
C11 NAA CWW HCW 5 0.00000 12.55000 0.00000
0.00000
NAA CWW CWW NAA 5 0.00000 44.98000 0.00000
0.00000
NAA CWW CWW HCW 5 0.00000 44.98000 0.00000
0.00000
HCW CWW CWW HCW 5 0.00000 44.98000 0.00000
0.00000
CWW NAA C11 H11 5 0.00000 0.00000 0.51900
0.00000
CRR NAA C11 H11 5 0.00000 0.00000 0.00000
0.00000
CWW NAA C11 C22 5 -7.15350 6.10640 0.79390
0.00000
CRR NAA C11 C22 5 -5.26910 0.00000 0.00000
0.00000
NAA C11 C22 CSS 5 -7.47970 3.16420 -1.20260
0.00000
NAA C11 C22 HCC 5 0.00000 0.00000 0.36700
0.00000
#define improper_CRR_CWW_NAA_C11 0.00000 8.37000 0.00000 0.00000
#define improper_NAA_NAA_CRR_HCR 0.00000 9.20000 0.00000 0.00000
#define improper_NAA_CWW_CWW_HCW 0.00000 9.20000 0.00000 0.00000
***************************** aminoacids.rtp
********************************
[ BMI ]
[ atoms ]
CW1 CWW -0.130 1
CW2 CWW -0.130 2
CRR CRR -0.110 3
HW1 HCW 0.210 4
HW2 HCW 0.210 5
HCR HCR 0.210 6
NA1 NAA 0.150 7
NA2 NAA 0.150 8
C11 C11 -0.170 9
H11 H11 0.130 10
H12 H11 0.130 11
C21 C22 0.010 12
HC1 HCC 0.060 13
HC2 HCC 0.060 14
CSS CSS -0.120 15
HC3 HCC 0.060 16
HC4 HCC 0.060 17
CTT CTT -0.180 18
HC5 HCC 0.060 19
HC6 HCC 0.060 20
HC7 HCC 0.060 21
C12 C11 -0.170 22
H13 H11 0.130 23
H14 H11 0.130 24
H15 H11 0.130 25
[ bonds ]
CW1 CW2
CW1 HW1
CW1 NA1
CW2 HW2
CW2 NA2
CRR HCR
CRR NA1
CRR NA2
NA1 C12
NA2 C11
C11 H11
C11 H12
C11 C21
C21 HC1
C21 HC2
C21 CSS
CSS HC3
CSS HC4
CSS CTT
CTT HC5
CTT HC6
CTT HC7
C12 H13
C12 H14
C12 H15
[ dihedrals ]
CW1 CW2 NA2 CRR
CW1 CW2 NA2 C11
CW1 NA1 CRR HCR
CW1 NA1 C12 H13
CW1 NA1 C12 H14
CW1 NA1 C12 H15
CW1 NA1 CRR HCR
CW1 NA1 CRR NA2
CW2 CW1 NA1 C12
CW2 CW1 NA1 CRR
CW2 NA2 CRR HCR
CW2 NA2 CRR NA1
CW2 NA2 C11 H11
CW2 NA2 C11 H12
CW2 NA2 C11 C21
CRR NA1 CW1 HW1
CRR NA1 C12 H13
CRR NA1 C12 H14
CRR NA1 C12 H15
CRR NA2 CW2 HW2
CRR NA2 C11 H11
CRR NA2 C11 H12
CRR NA2 C11 C21
HW1 CW1 CW2 HW2
HW1 CW1 CW2 NA2
HW1 CW1 NA1 C12
HW2 CW2 CW1 NA1
HW2 CW2 NA2 C11
HCR CRR NA1 C12
HCR CRR NA2 C11
NA1 CRR NA2 C11
NA1 CW1 CW2 NA2
NA2 CRR NA1 C12
NA2 C11 C21 HC1
NA2 C11 C21 HC2
NA2 C11 C21 CSS
C11 C21 CSS HC3
C11 C21 CSS HC4
C11 C21 CSS CTT
H11 C11 C21 HC1
H11 C11 C21 HC2
H11 C11 C21 CSS
H12 C11 C21 HC1
H12 C11 C21 HC2
H12 C11 C21 CSS
C21 CSS CTT HC5
C21 CSS CTT HC6
C21 CSS CTT HC7
HC1 C21 CSS HC3
HC1 C21 CSS HC4
HC1 C21 CSS CTT
HC2 C21 CSS HC3
HC2 C21 CSS HC4
HC2 C21 CSS CTT
HC3 CSS CTT HC5
HC3 CSS CTT HC6
HC3 CSS CTT HC7
HC4 CSS CTT HC5
HC4 CSS CTT HC6
HC4 CSS CTT HC7
[ dihedrals ]
CRR CW1 NA1 C12 improper_CRR_CWW_NAA_C11
CRR NA2 CW2 C11 improper_CRR_NAA_CWW_C11
NA1 NA2 CRR HCR improper_NAA_NAA_CRR_HCR
NA1 CW1 CW2 HW1 improper_NAA_CWW_CWW_HCW
NA2 CW2 CW1 HW2 improper_NAA_CWW_CWW_HCW
[ Cll ]
[ atoms ]
Cll Cll -1.000 0
*************************atomtypes.atp*******************
CWW 12.01100
CRR 12.01100
NAA 14.00700
C11 12.01100
C22 12.01100
CSS 12.01100
CTT 12.01100
HCC 1.00800
HCR 1.00800
HCW 1.00800
H11 1.00800
Cll 35.45300
*************************** ffbonded.itp ******************
;[ bondtypes ]
CTT CSS 1 0.15290 224200
CSS C22 1 0.15290 224200
C22 C11 1 0.15290 224200
HCC CTT 1 0.10900 -284500
HCC CSS 1 0.10900 -284500
HCC C22 1 0.10900 -284500
HCC C11 1 0.10900 -284500
H11 C11 1 0.10900 -284500
CRR HCR 1 0.1080 -284500
CWW HCW 1 0.1080 -284500
CRR NAA 1 0.1315 399200
CWW NAA 1 0.1378 357400
CWW CWW 1 0.1341 435200
NAA C11 1 0.1466 141000
;angletypes
CTT CSS C22 1 112.700 488.300
CSS C22 C11 1 112.700 488.300
C22 C11 NAA 1 112.700 488.300
CSS CTT HCC 1 110.700 313.800
CTT CSS HCC 1 110.700 313.800
C22 CSS HCC 1 110.700 313.800
C22 C11 H11 1 110.700 313.800
C11 C22 HCC 1 110.700 313.800
CSS C22 HCC 1 110.700 313.800
HCC CTT HCC 1 107.800 276.100
HCC CSS HCC 1 107.800 276.100
HCC C22 HCC 1 107.800 276.100
H11 C11 H11 1 107.800 276.100
CWW NAA CRR 1 108.000 585.800
CWW NAA C11 1 125.600 585.800
CRR NAA C11 1 126.400 585.800
NAA CRR HCR 1 125.100 292.900
NAA CRR NAA 1 109.800 585.800
NAA CWW CWW 1 107.100 585.800
NAA CWW HCW 1 122.000 292.900
CWW CWW HCW 1 130.900 292.900
NAA C11 H11 1 110.700 313.800
NAA C11 C22 1 112.700 488.300
;dihedraltypes
HCC CTT CSS HCC 5 0.00000 0.00000 1.33050 0.00000
HCC CSS C22 HCC 5 0.00000 0.00000 1.33050 0.00000
HCC C22 C11 H11 5 0.00000 0.00000 1.33050 0.00000
CTT CSS C22 HCC 5 0.00000 0.00000 1.53130 0.00000
CSS C22 C11 H11 5 0.00000 0.00000 1.53130 0.00000
C11 C22 CSS HCC 5 0.00000 0.00000 1.53130 0.00000
C22 CSS CTT HCC 5 0.00000 0.00000 1.53130 0.00000
CTT CSS C22 C11 5 7.28000 -0.65690 1.16730
0.00000
CWW NAA CRR NAA 5 0.00000 19.46000 0.00000
0.00000
CWW NAA CRR HCR 5 0.00000 19.46000 0.00000
0.00000
C11 NAA CRR NAA 5 0.00000 19.46000 0.00000
0.00000
C11 NAA CRR HCR 5 0.00000 19.46000 0.00000
0.00000
CRR NAA CWW CWW 5 0.00000 12.55000 0.00000
0.00000
CRR NAA CWW HCW 5 0.00000 12.55000 0.00000
0.00000
C11 NAA CWW CWW 5 0.00000 12.55000 0.00000
0.00000
C11 NAA CWW HCW 5 0.00000 12.55000 0.00000
0.00000
NAA CWW CWW NAA 5 0.00000 44.98000 0.00000
0.00000
NAA CWW CWW HCW 5 0.00000 44.98000 0.00000
0.00000
HCW CWW CWW HCW 5 0.00000 44.98000 0.00000
0.00000
CWW NAA C11 H11 5 0.00000 0.00000 0.51900
0.00000
CRR NAA C11 H11 5 0.00000 0.00000 0.00000
0.00000
CWW NAA C11 C22 5 -7.15350 6.10640 0.79390
0.00000
CRR NAA C11 C22 5 -5.26910 0.00000 0.00000
0.00000
NAA C11 C22 CSS 5 -7.47970 3.16420 -1.20260
0.00000
NAA C11 C22 HCC 5 0.00000 0.00000 0.36700 0.00000
#define improper_CRR_CWW_NAA_C11 0.00000 8.37000 0.00000 0.00000
#define improper_NAA_NAA_CRR_HCR 0.00000 9.20000 0.00000 0.00000
#define improper_NAA_CWW_CWW_HCW 0.00000 9.20000 0.00000 0.00000
#define improper_CRR_NAA_CWW_C11 0.00000 8.37000 0.00000 0.00000
*********************************ffnonbonded.itp***********************************
;[ atomtypes ]
CWW CWW 6 12.01100 -0.130 A 0.3550 0.29288
CRR CRR 6 12.01100 -0.110 A 0.3550 0.29288
HCW HCW 1 1.00800 0.210 A 0.2420 0.12552
HCR HCR 1 1.00800 0.210 A 0.2420 0.12552
NAA NAA 7 14.00670 0.150 A 0.3250 0.71128
C11 C11 6 12.01100 -0.170 A 0.3500 0.27614
H11 H11 1 1.00800 0.130 A 0.2500 0.12552
C22 C22 6 12.01100 0.010 A 0.3500 0.27614
HCC HCC 1 1.00800 0.060 A 0.2500 0.12552
CSS CSS 6 12.01100 -0.120 A 0.3500 0.27614
CTT CTT 6 12.01100 -0.180 A 0.3500 0.27614
Cll Cll 17 35.45300 -1.000 A 0.3650 0.8300053
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