Hello people, so I am working on MOFs adsoprtion on CO2 but the issues lies that the forcefield file which I made by taking UFF/Dreiding and OPLS Parameters is giving me no vdw warnings. For an example, check my cubtc test files: cif file portion
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_charge
Cu1 Cu 0.2853 0.2853 0.0000 1.248
O1 O_MOF 0.3166 0.2431 0.9478 -0.624
C1 C_MOF 0.2968 0.2032 0.9313 0.494
C2 C_MOF 0.3220 0.1780 0.8870 0.130
C3 C_MOF 0.3655 0.1994 0.8655 -0.156
H1 H_MOF 0.3802 0.2280 0.8802 0.156
forcefield mixing:# general rule for shifted vs truncated
truncated
# general rule tailcorrections
no
# number of defined interactions
33
# type interaction
O_CO2 lennard-jones 79.0 3.05
C_CO2 lennard-jones 27.0 2.80
Cu lennard-jones 2.5161 3.11369
C_MOF lennard-jones 47.8562 3.47299
O_MOF lennard-jones 48.1581 3.03315
H_MOF lennard-jones 7.64893 2.84642
N_BMIM lennard-jones 85.55 3.25
C_BMIM_CR lennard-jones 35.22 3.55
C_BMIM_CW lennard-jones 35.22 3.55
H_BMIM_HR lennard-jones 15.10 2.42
H_BMIM_HW lennard-jones 15.10 2.42
C_BMIM_CM lennard-jones 33.21 3.50
H_BMIM_HM lennard-jones 15.10 2.50
C_BMIM_CA lennard-jones 33.21 3.50
H_BMIM_HA lennard-jones 15.10 2.50
C_BMIM_CS lennard-jones 33.21 3.50
H_BMIM_HS lennard-jones 15.10 2.50
C_BMIM_CT lennard-jones 33.21 3.50
H_BMIM_HT lennard-jones 15.10 2.50
B_BF4 lennard-jones 47.81 3.581
F_BF4 lennard-jones 30.70 3.118
OwH2O_TIP4P lennard-jones 78.0 3.154
HwH2O_TIP4P none
MwH2O_TIP4P none
OwH2O_TIP4PEW lennard-jones 81.9 3.164
HwH2O_TIP4PEW none
MwH2O_TIP4PEW none
OwH2O_TIP5P lennard-jones 80.52 3.12
HwH2O_TIP5P none
MwH2O_TIP5P none
OwH2O_TIP5PEW lennard-jones 89.57 3.097
HwH2O_TIP5PEW none
MwH2O_TIP5PEW none
# general mixing rule for Lennard-Jones
Lorentz-Berthelot
pseudo atoms def
#number of pseudo atoms
33
#type print as chem oxidation mass charge polarization B-factor radii connectivity anisotropic anisotropic-type tinker-type
O_CO2 yes O O 0 15.9996 -0.350 0.0 1.0 1.0 1 0 absolute 0
C_CO2 yes C C 0 12.0110 0.700 0.0 1.0 1.0 2 0 absolute 0
Cu yes Cu Cu 0 63.5460 0.8360 0.0 1.0 1.0 5 0 absolute 0
C_MOF yes C C 0 12.0110 0.4170 0.0 1.0 1.0 3 0 absolute 0
O_MOF yes O O 0 15.9996 -0.8340 0.0 1.0 1.0 3 0 absolute 0
H_MOF yes H H 0 1.0080 0.4170 0.0 1.0 1.0 1 0 absolute 0
N_BMIM yes N N 0 14.0070 0.1760 0.0 1.0 1.0 3 0 absolute 0
C_BMIM_CR yes C C 0 12.0110 -0.0720 0.0 1.0 1.0 3 0 absolute 0
C_BMIM_CW yes C C 0 12.0110 -0.1920 0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HR yes H H 0 1.0080 0.1680 0.0 1.0 1.0 1 0 absolute 0
H_BMIM_HW yes H H 0 1.0080 0.2160 0.0 1.0 1.0 1 0 absolute 0
C_BMIM_CM yes C C 0 12.0110 -0.2800 0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HM yes H H 0 1.0080 0.1440 0.0 1.0 1.0 1 0 absolute 0
C_BMIM_CA yes C C 0 12.0110 -0.1360 0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HA yes H H 0 1.0080 0.1440 0.0 1.0 1.0 1 0 absolute 0
C_BMIM_CS yes C C 0 12.0110 -0.0960 0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HS yes H H 0 1.0080 0.0480 0.0 1.0 1.0 1 0 absolute 0
C_BMIM_CT yes C C 0 12.0110 -0.1920 0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HT yes H H 0 1.0080 0.0640 0.0 1.0 1.0 1 0 absolute 0
B_BF4 yes B B 0 10.8110 1.1340 0.0 1.0 1.0 3 0 absolute 0
F_BF4 yes F F 0 18.9980 -0.5335 0.0 1.0 1.0 1 0 absolute 0
OwH2O_TIP4P yes O O 0 15.9996 0.0000 0.0 1.0 1.0 3 0 absolute 0
HwH2O_TIP4P yes H H 0 1.0008 0.5200 0.0 1.0 1.0 1 0 absolute 0
MwH2O_TIP4P yes M - 0 0.0000 -1.0400 0.0 1.0 1.0 1 0 absolute 0
OwH2O_TIP4PEW yes O O 0 15.9996 0.0000 0.0 1.0 1.0 3 0 absolute 0
HwH2O_TIP4PEW yes H H 0 1.0008 0.52422 0.0 1.0 1.0 1 0 absolute 0
MwH2O_TIP4PEW yes M - 0 0.0000 -1.04844 0.0 1.0 1.0 1 0 absolute 0
OwH2O_TIP5P yes O O 0 15.9996 0.0000 0.0 1.0 1.0 3 0 absolute 0
HwH2O_TIP5P yes H H 0 1.0008 0.2410 0.0 1.0 1.0 1 0 absolute 0
MwH2O_TIP5P yes M - 0 0.0000 -0.2410 0.0 1.0 1.0 1 0 absolute 0
OwH2O_TIP5PEW yes O O 0 15.9996 0.0000 0.0 1.0 1.0 3 0 absolute 0
HwH2O_TIP5PEW yes H H 0 1.0008 0.2410 0.0 1.0 1.0 1 0 absolute 0
MwH2O_TIP5PEW yes M - 0 0.0000 -0.2410 0.0 1.0 1.0 1 0 absolute 0
and in output getting:
WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION O_CO2-Cu1 O_CO2-O1 O_CO2-C1 O_CO2-C2 O_CO2-C3 O_CO2-H1 C_CO2-Cu1 C_CO2-O1 C_CO2-C1 C_CO2-C2 C_CO2-C3 C_CO2-H1 Cu1-O_CO2 Cu1-C_CO2 Cu1-O1 Cu1-C1 Cu1-C2 Cu1-C3 Cu1-H1 O1-O_CO2 O1-C_CO2 O1-Cu1 O1-C1 O1-C2 O1-C3 O1-H1 C1-O_CO2 C1-C_CO2 C1-Cu1 C1-O1 C1-C2 C1-C3 C1-H1 C2-O_CO2 C2-C_CO2 C2-Cu1 C2-O1 C2-C1 C2-C3 C2-H1 C3-O_CO2 C3-C_CO2 C3-Cu1 C3-O1 C3-C1 C3-C2 C3-H1 H1-O_CO2 H1-C_CO2 H1-Cu1 (maximum 50 interactions shown)
I will be working on many mofs so assigning each one a charge might not be efficient. I am using no charges from cif file itself as modifying many MOFs with ILs liquid and such reduces the charges to zero with conversions.
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_charge
Cu1 Cu 0.2853 0.2853 0.0000 1.248
O1 O_MOF 0.3166 0.2431 0.9478 -0.624
C1 C_MOF 0.2968 0.2032 0.9313 0.494
C2 C_MOF 0.3220 0.1780 0.8870 0.130
C3 C_MOF 0.3655 0.1994 0.8655 -0.156
H1 H_MOF 0.3802 0.2280 0.8802 0.156
forcefield mixing:# general rule for shifted vs truncated
truncated
# general rule tailcorrections
no
# number of defined interactions
33
# type interaction
O_CO2 lennard-jones 79.0 3.05
C_CO2 lennard-jones 27.0 2.80
Cu lennard-jones 2.5161 3.11369
C_MOF lennard-jones 47.8562 3.47299
O_MOF lennard-jones 48.1581 3.03315
H_MOF lennard-jones 7.64893 2.84642
N_BMIM lennard-jones 85.55 3.25
C_BMIM_CR lennard-jones 35.22 3.55
C_BMIM_CW lennard-jones 35.22 3.55
H_BMIM_HR lennard-jones 15.10 2.42
H_BMIM_HW lennard-jones 15.10 2.42
C_BMIM_CM lennard-jones 33.21 3.50
H_BMIM_HM lennard-jones 15.10 2.50
C_BMIM_CA lennard-jones 33.21 3.50
H_BMIM_HA lennard-jones 15.10 2.50
C_BMIM_CS lennard-jones 33.21 3.50
H_BMIM_HS lennard-jones 15.10 2.50
C_BMIM_CT lennard-jones 33.21 3.50
H_BMIM_HT lennard-jones 15.10 2.50
B_BF4 lennard-jones 47.81 3.581
F_BF4 lennard-jones 30.70 3.118
OwH2O_TIP4P lennard-jones 78.0 3.154
HwH2O_TIP4P none
MwH2O_TIP4P none
OwH2O_TIP4PEW lennard-jones 81.9 3.164
HwH2O_TIP4PEW none
MwH2O_TIP4PEW none
OwH2O_TIP5P lennard-jones 80.52 3.12
HwH2O_TIP5P none
MwH2O_TIP5P none
OwH2O_TIP5PEW lennard-jones 89.57 3.097
HwH2O_TIP5PEW none
MwH2O_TIP5PEW none
# general mixing rule for Lennard-Jones
Lorentz-Berthelot
pseudo atoms def
#number of pseudo atoms
33
#type print as chem oxidation mass charge polarization B-factor radii connectivity anisotropic anisotropic-type tinker-type
O_CO2 yes O O 0 15.9996 -0.350 0.0 1.0 1.0 1 0 absolute 0
C_CO2 yes C C 0 12.0110 0.700 0.0 1.0 1.0 2 0 absolute 0
Cu yes Cu Cu 0 63.5460 0.8360 0.0 1.0 1.0 5 0 absolute 0
C_MOF yes C C 0 12.0110 0.4170 0.0 1.0 1.0 3 0 absolute 0
O_MOF yes O O 0 15.9996 -0.8340 0.0 1.0 1.0 3 0 absolute 0
H_MOF yes H H 0 1.0080 0.4170 0.0 1.0 1.0 1 0 absolute 0
N_BMIM yes N N 0 14.0070 0.1760 0.0 1.0 1.0 3 0 absolute 0
C_BMIM_CR yes C C 0 12.0110 -0.0720 0.0 1.0 1.0 3 0 absolute 0
C_BMIM_CW yes C C 0 12.0110 -0.1920 0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HR yes H H 0 1.0080 0.1680 0.0 1.0 1.0 1 0 absolute 0
H_BMIM_HW yes H H 0 1.0080 0.2160 0.0 1.0 1.0 1 0 absolute 0
C_BMIM_CM yes C C 0 12.0110 -0.2800 0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HM yes H H 0 1.0080 0.1440 0.0 1.0 1.0 1 0 absolute 0
C_BMIM_CA yes C C 0 12.0110 -0.1360 0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HA yes H H 0 1.0080 0.1440 0.0 1.0 1.0 1 0 absolute 0
C_BMIM_CS yes C C 0 12.0110 -0.0960 0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HS yes H H 0 1.0080 0.0480 0.0 1.0 1.0 1 0 absolute 0
C_BMIM_CT yes C C 0 12.0110 -0.1920 0.0 1.0 1.0 3 0 absolute 0
H_BMIM_HT yes H H 0 1.0080 0.0640 0.0 1.0 1.0 1 0 absolute 0
B_BF4 yes B B 0 10.8110 1.1340 0.0 1.0 1.0 3 0 absolute 0
F_BF4 yes F F 0 18.9980 -0.5335 0.0 1.0 1.0 1 0 absolute 0
OwH2O_TIP4P yes O O 0 15.9996 0.0000 0.0 1.0 1.0 3 0 absolute 0
HwH2O_TIP4P yes H H 0 1.0008 0.5200 0.0 1.0 1.0 1 0 absolute 0
MwH2O_TIP4P yes M - 0 0.0000 -1.0400 0.0 1.0 1.0 1 0 absolute 0
OwH2O_TIP4PEW yes O O 0 15.9996 0.0000 0.0 1.0 1.0 3 0 absolute 0
HwH2O_TIP4PEW yes H H 0 1.0008 0.52422 0.0 1.0 1.0 1 0 absolute 0
MwH2O_TIP4PEW yes M - 0 0.0000 -1.04844 0.0 1.0 1.0 1 0 absolute 0
OwH2O_TIP5P yes O O 0 15.9996 0.0000 0.0 1.0 1.0 3 0 absolute 0
HwH2O_TIP5P yes H H 0 1.0008 0.2410 0.0 1.0 1.0 1 0 absolute 0
MwH2O_TIP5P yes M - 0 0.0000 -0.2410 0.0 1.0 1.0 1 0 absolute 0
OwH2O_TIP5PEW yes O O 0 15.9996 0.0000 0.0 1.0 1.0 3 0 absolute 0
HwH2O_TIP5PEW yes H H 0 1.0008 0.2410 0.0 1.0 1.0 1 0 absolute 0
MwH2O_TIP5PEW yes M - 0 0.0000 -0.2410 0.0 1.0 1.0 1 0 absolute 0
and in output getting:
WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION O_CO2-Cu1 O_CO2-O1 O_CO2-C1 O_CO2-C2 O_CO2-C3 O_CO2-H1 C_CO2-Cu1 C_CO2-O1 C_CO2-C1 C_CO2-C2 C_CO2-C3 C_CO2-H1 Cu1-O_CO2 Cu1-C_CO2 Cu1-O1 Cu1-C1 Cu1-C2 Cu1-C3 Cu1-H1 O1-O_CO2 O1-C_CO2 O1-Cu1 O1-C1 O1-C2 O1-C3 O1-H1 C1-O_CO2 C1-C_CO2 C1-Cu1 C1-O1 C1-C2 C1-C3 C1-H1 C2-O_CO2 C2-C_CO2 C2-Cu1 C2-O1 C2-C1 C2-C3 C2-H1 C3-O_CO2 C3-C_CO2 C3-Cu1 C3-O1 C3-C1 C3-C2 C3-H1 H1-O_CO2 H1-C_CO2 H1-Cu1 (maximum 50 interactions shown)
I will be working on many mofs so assigning each one a charge might not be efficient. I am using no charges from cif file itself as modifying many MOFs with ILs liquid and such reduces the charges to zero with conversions.