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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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