GROMACS version:2022.1 and 2020.1
GROMACS modification: Yes/No
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Hello everyone.
I want to investigate the behavior of two small molecules in acetonitrile and chloroform. I downloaded the ITP and PDB files of acetonitrile from “virtualchemistry”. I put my molecules in the box and tried to solvate with the command “gmx solvate -cp box. gro -cs acetonitrile_T298.15.pdb -p Topol.top -o solvated.gro”. Also, I included the ITP file in the topology. I used gromacs 2022.1 and 2020.1.
Unfortunately, when I opened the solvated.gro file via VMD, I saw the solvent molecules falling apart and could not fix this problem. I changed some parameters in the ITP file and PDB file but I was not successful. I sent the files and pictures of my system. I hope you can guide me to solve this problem.
the itp file:
; This include topology was generated for the paper below:
; Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub,
; Luciano T. Costa and David van der Spoel
; Force Field Benchmark of Organic Liquids: Density,
; Enthalpy of Vaporization, Heat Capacities, Surface Tension,
; Isothermal Compressibility, Volumetric Expansion Coefficient,
; and Dielectric Constant
; J. Chem. Theor. Comput. 8 (2012) 61-74
; http://dx.doi.org/10.1021/ct200731v
; REFERENCE Caleman2012a
; Corrected nrexcl to 3. DvdS, 2011-09-12
[ moleculetype ]
; Name nrexcl
acetonitrile 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 opls_755 1 MOL C 1 -0.08 13.8574 ; qtot 0
2 opls_759 2 MOL H 1 0.06 1.0079 ; qtot 0
3 opls_759 3 MOL H 1 0.06 1.0079 ; qtot 0
4 opls_759 4 MOL H 1 0.06 1.0079 ; qtot 0
5 opls_754 5 MOL C 2 0.46 0 ; qtot 0
6 opls_753 6 MOL N 3 -0.56 0 ; qtot 0
7 ML 1 MOL ML 4 0 24.1707 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
#ifdef NORMALMODES
[ bonds ]
; ai aj funct c0 c1
1 7 1 2.232581e-01 1e7
#else
[ constraints ]
; ai aj funct c0 c1
1 7 1 2.232581e-01 0.000000e+00
#endif
[ exclusions ]
; i excluded from i
1 2 3 4 5
2 1
3 1
4 1
5 1 6 2 3 4
6 6 5 1
7 7
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
[ virtual_sites2 ]
; ai aj ak funct c0
5 1 7 1 6.517123e-01
6 1 7 1 1.166811e+00
and the pdb file:
COMPND acetonitrile LIQ
REMARK Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub,
REMARK Luciano T. Costa and David van der Spoel
REMARK Force Field Benchmark of Organic Liquids: Density,
REMARK Enthalpy of Vaporization, Heat Capacities, Surface Tension,
REMARK Isothermal Compressibility, Volumetric Expansion Coefficient,
REMARK and Dielectric Constant
REMARK J. Chem. Theory Comput. 8 (2012) 61-74
REMARK http://dx.doi.org/10.1021/ct200731v
REMARK REFERENCE Caleman2012a
AUTHOR GENERATED BY OPEN BABEL 2.3.90
CRYST1 44.848 44.848 44.848 90.00 90.00 90.00 P1 1
ATOM 1 C MOL A 1 0.230 29.490 3.150 1.00 0.00 C
ATOM 2 H MOL A 2 -0.200 28.650 2.600 1.00 0.00 H
ATOM 3 H MOL A 3 0.080 30.330 2.470 1.00 0.00 H
ATOM 4 H MOL A 4 1.270 29.380 3.430 1.00 0.00 H
ATOM 5 C MOL A 5 -0.390 29.780 4.430 1.00 0.00 C
ATOM 6 N MOL A 6 -0.880 30.010 5.450 1.00 0.00 N
ATOM 7 ML MOL A 1 -0.720 29.940 5.120 1.00 0.00 Xx
ATOM 8 C MOL A 1 31.280 27.740 1.970 1.00 0.00 C
ATOM 9 H MOL A 2 31.510 27.110 1.100 1.00 0.00 H
ATOM 10 H MOL A 3 31.870 27.480 2.840 1.00 0.00 H
ATOM 11 H MOL A 4 30.220 27.940 2.120 1.00 0.00 H
ATOM 12 C MOL A 5 31.890 29.000 1.590 1.00 0.00 C
ATOM 13 N MOL A 6 32.380 30.000 1.290 1.00 0.00 N
ATOM 14 ML MOL A 1 32.220 29.680 1.390 1.00 0.00 Xx
ATOM 15 C MOL A 1 4.630 2.160 35.260 1.00 0.00 C
ATOM 16 H MOL A 2 4.370 1.100 35.270 1.00 0.00 H
ATOM 17 H MOL A 3 5.430 2.390 34.550 1.00 0.00 H
ATOM 18 H MOL A 4 4.820 2.640 36.210 1.00 0.00 H
ATOM 19 C MOL A 5 3.370 2.720 34.790 1.00 0.00 C
ATOM 20 N MOL A 6 2.380 3.160 34.420 1.00 0.00 N
ATOM 21 ML MOL A 1 2.700 3.020 34.540 1.00 0.00 Xx
.
.
.
ATOM 6987 C MOL A 1 0.220 6.210 32.780 1.00 0.00 C
ATOM 6988 H MOL A 2 0.180 5.570 31.900 1.00 0.00 H
ATOM 6989 H MOL A 3 0.370 5.550 33.640 1.00 0.00 H
ATOM 6990 H MOL A 4 -0.750 6.670 32.940 1.00 0.00 H
ATOM 6991 C MOL A 5 1.230 7.240 32.610 1.00 0.00 C
ATOM 6992 N MOL A 6 2.040 8.050 32.480 1.00 0.00 N
ATOM 6993 ML MOL A 1 1.780 7.790 32.530 1.00 0.00 Xx
ATOM 6994 C MOL A 1 3.120 4.090 7.850 1.00 0.00 C
ATOM 6995 H MOL A 2 2.720 3.120 7.570 1.00 0.00 H
ATOM 6996 H MOL A 3 3.080 4.780 7.010 1.00 0.00 H
ATOM 6997 H MOL A 4 4.210 4.050 7.940 1.00 0.00 H
ATOM 6998 C MOL A 5 2.610 4.570 9.130 1.00 0.00 C
ATOM 6999 N MOL A 6 2.200 4.950 10.140 1.00 0.00 N
ATOM 7000 ML MOL A 1 2.330 4.830 9.810 1.00 0.00 Xx
CONECT 1 3 2 4
CONECT 2 1
CONECT 3 1
.
.
.
MASTER 0 0 0 0 0 0 0 0 7000 0 7000 0
END