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Add parameters for adsorbed molecules #11

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Add parameters for adsorbed molecules #11

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4 changes: 3 additions & 1 deletion ForceFields/DREIDING/force_field_mixing_rules.def
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ shifted
# general rule tailcorrections
no
# number of defined interactions
49
51
# type, interaction, epsilon [K], sigma [A] IMPORTANT: define shortest matches first, so that more specific ones overwrites these
H_ lennard-jones 7.648938 2.84642 // DREIDING S.L. Mayo et al., J. Phys. Chem. 1990, 94, 8897-8909.
B_ lennard-jones 47.8058 3.58141 // DREIDING
Expand Down Expand Up @@ -54,5 +54,7 @@ Lw_T5 none // idem
Hw_T5 none // idem
S_so2 lennard-jones 73.8 3.39 // J. Phys. Chem. B 2011, 115, 17, 4949–4954
O_so2 lennard-jones 79.0 3.05 // J. Phys. Chem. B 2011, 115, 17, 4949–4954
Ow_spce lennard-jones 78.15 3.166 // J. Phys. Chem. A 2001, 105, 9954-9960
Hw_spce none
# general mixing rule for Lennard-Jones
Lorentz-Berthelot
6 changes: 4 additions & 2 deletions ForceFields/DREIDING/pseudo_atoms.def
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#number of pseudo atoms
49
51
#type print as chem oxidation mass charge polarization B-factor radii connectivity anisotropic anisotropic-type tinker-type
H yes H H 0 1.00794 0.0 0.0 1.0 0.250 0 0 relative 0
B yes B B 0 10.81100 0.0 0.0 1.0 0.850 0 0 relative 0
Expand Down Expand Up @@ -49,4 +49,6 @@ Ow_T4ew yes O O 0 15.99940 0.000 0.0 1.0
Hw_T4ew yes H H 0 1.00794 0.5242 0.0 1.0 1.00 0 0 relative 0
M_T4ew no L - 0 0.00000 -1.04844 0.0 1.0 1.00 0 0 relative 0
O_so2 yes O O 0 15.99940 -0.295 0.0 1.0 0.730 0 0 relative 0
S_so2 yes S S 0 32.06500 0.59 0.0
S_so2 yes S S 0 32.06500 0.59 0.0 1.0 0.730 0 0 relative 0
Ow_spce yes O O 0 15.99940 -0.8476 0.0 1.0 1.00 0 0 relative 0
Hw_spce yes H H 0 1.00794 0.4238 0.0 1.0 1.00 0 0 relative 0
23 changes: 23 additions & 0 deletions ForceFields/MoleculeDefinitions/SPC-E.def
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@@ -0,0 +1,23 @@
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
623.0 // W. C. Volker, The Journal of Chemical Physics 146.5 (2017)
13400000 // W. C. Volker, The Journal of Chemical Physics 146.5 (2017)
0.580722 // W. C. Volker, The Journal of Chemical Physics 146.5 (2017)
# total number Of atoms
3
# number of groups
1
# water-group
rigid
# number of atoms
3
# atomic positions
0 Ow_spce 0.00000000 0.00000000 0.00000000
1 Hw_spce 0.65806264 -0.75296318 0.00000000
2 Hw_spce 0.49056485 0.87140469 0.00000000
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 2 0 0 0 0 0 0 0 0 0 0 0 0 0
# Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
0 2 RIGID_BOND
# Number of config moves
0
4 changes: 3 additions & 1 deletion ForceFields/UFF/force_field_mixing_rules.def
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ shifted
# general rule tailcorrections
no
# number of defined interactions
122
124
# type, interaction, epsilon [K], sigma [A] IMPORTANT: define shortest matches first, so that more specific ones overwrites these
C_ lennard-jones 52.83806 3.43085 // UFF A.K. Rappé et al., J. Am. Chem. Soc. 1992, 114, 10024-10035.
O_ lennard-jones 30.19317 3.11815 //
Expand Down Expand Up @@ -127,5 +127,7 @@ Lw_T5 none // idem
Hw_T5 none // idem
S_so2 lennard-jones 73.8 3.39 // J. Phys. Chem. B 2011, 115, 17, 4949–4954
O_so2 lennard-jones 79.0 3.05 // J. Phys. Chem. B 2011, 115, 17, 4949–4954
Ow_spce lennard-jones 78.15 3.166 // J. Phys. Chem. A 2001, 105, 9954-9960
Hw_spce none
# general mixing rule for Lennard-Jones
Lorentz-Berthelot
6 changes: 4 additions & 2 deletions ForceFields/UFF/pseudo_atoms.def
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#number of pseudo atoms
122
124
#type print as chem oxidation mass charge polarization B-factor radii connectivity anisotropic anisotropic-type tinker-type
C yes C C 0 12.01070 0.0 0.0 1.0 0.770 0 0 relative 0
O yes O O 0 15.99940 0.0 0.0 1.0 0.730 0 0 relative 0
Expand Down Expand Up @@ -122,4 +122,6 @@ Ow_T4ew yes O O 0 15.99940 0.000 0.0 1.0
Hw_T4ew yes H H 0 1.00794 0.5242 0.0 1.0 1.00 0 0 relative 0
M_T4ew no L - 0 0.00000 -1.04844 0.0 1.0 1.00 0 0 relative 0
O_so2 yes O O 0 15.99940 -0.295 0.0 1.0 0.730 0 0 relative 0
S_so2 yes S S 0 32.06500 0.59 0.0 1.0 1.020 0 0 relative 0
S_so2 yes S S 0 32.06500 0.59 0.0 1.0 1.020 0 0 relative 0
Ow_spce yes O O 0 15.99940 -0.8476 0.0 1.0 1.00 0 0 relative 0
Hw_spce yes H H 0 1.00794 0.4238 0.0 1.0 1.00 0 0 relative 0