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Merge pull request #33 from molssi-seamm/dev
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Fixed bugs and added parameters for imidazolium cations
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@seamm
seamm authored Sep 14, 2023
2 parents fcb9ebb + 261bf23 commit 7cc8892
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5 changes: 5 additions & 0 deletions HISTORY.rst
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History
=======

2023.9.14 -- Fixed errors! And added C2mim to test.
* The units of the torsions were incorrect in the last implementation.
* Added parameters for 1-alkyl-3-methylimidazolium cations from JCP 108, 2038 (2004)
* Tested much more thoroughly.

2023.9.13 -- Added parameters for TFSI to CL&P/OPLSAA
* Parameters for TFSI - bis[(trifluoromethyl)sulfonyl]imide

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272 changes: 265 additions & 7 deletions forcefield_step/data/oplsaa.frc
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Expand Up @@ -10768,6 +10768,86 @@
"description": "F in bis(trifluormethanesulfonyl)imide",
"overrides": []
}
},
"NA": {
"2023.09.14": {
"smarts": [
"C[n:1]1cc[n:2](c1)C",
"C[n:1]1cc[n+:2](c1)C"
],
"description": "ring N 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"CR": {
"2023.09.14": {
"smarts": [
"Cn1cc[n]([c:1]1)C",
"Cn1cc[n+]([c:1]1)C"
],
"description": "ring single C 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"CW": {
"2023.09.14": {
"smarts": [
"Cn1[c:1][c:2][n](c1)C",
"Cn1[c:1][c:2][n+](c1)C"
],
"description": "ring pair of C's 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"HA": {
"2023.09.14": {
"smarts": [
"Cn1c([H:1])c([H:2])[n](c1([H:3]))C",
"Cn1c([H:1])c([H:2])[n+](c1([H:3]))C"
],
"description": "ring N 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"C1": {
"2023.09.14": {
"smarts": [
"[C:1]n1cc[n](c1)[C:2]",
"[C:1]n1cc[n+](c1)[C:2]"
],
"description": "alkyl carbon bonded to N 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"H1": {
"2023.09.14": {
"smarts": [
"C([H:1])n1cc[n](c1)C[H:2]",
"C([H:1])n1cc[n+](c1)C[H:2]"
],
"description": "H on alkyl C bonded to N 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"C2": {
"2023.09.14": {
"smarts": [
"C[C:1]Cn1cc[n](c1)C",
"C[C:1]Cn1cc[n+](c1)C"
],
"description": "methylene C 2 from N 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"CE": {
"2023.09.14": {
"smarts": [
"[CH3:1]Cn1cc[n](c1)C",
"[CH3:1]Cn1cc[n+](c1)C"
],
"description": "methyl C 2 from N 1-ethyl-3-methylimidazolium cation",
"overrides": []
}
}
}

Expand All @@ -10789,6 +10869,17 @@
2023.09.13 5 Fbt 18.998 F 1 F in bis(trifluoromethanesulfonyl)imide anion
2023.09.13 5 Obt 15.999 O 1 O in bis(trifluoromethanesulfonyl)imide anion
2023.09.13 5 Cbt 15.999 C 4 C in bis(trifluoromethanesulfonyl)imide anion
2023.09.14 2 C1 12.011 C 4 C bonded to N in charged imidazolium group
2023.09.14 2 C2 12.011 C 4 C to C bonded to N in charged imidazolium group
2023.09.14 2 CE 12.011 C 4 methyl carbon in ethane bonded to N in charged imidazolium group
2023.09.14 2 CR 12.011 C 3 C between N's in charged imidazolium group
2023.09.14 2 CS 12.011 C 4 Secondary C in side chain bonded to N in charged imidazolium group
2023.09.14 2 CT 12.011 C 4 Terminal C in side chain bonded to N in charged imidazolium group
2023.09.14 2 CW 12.011 C 3 The pair of C on longer side bonded to N in charged imidazolium group
2023.09.14 2 HA 1.008 H 1 H bonded to ring C in charged imidazolium group
2023.09.14 2 HC 1.008 H 1 H bonded to side chain C past first in charged imidazolium group
2023.09.14 2 H1 1.008 H 1 H bonded to first side chain C in charged imidazolium group
2023.09.14 2 NA 14.007 N 2 N in charged imidazolium group


#equivalence CL&P
Expand All @@ -10805,6 +10896,19 @@
2023.09.13 5 Fbt Fbt Fbt Fbt Fbt Fbt
2023.09.13 5 Obt Obt O O O O
2023.09.13 5 Cbt Cbt C C C C
2023.09.14 2 C1 C1 opls_18 opls_18 opls_18 opls_18
2023.09.14 2 C2 C2 opls_18 opls_18 opls_18 opls_18
2023.09.14 2 CE CE opls_18 opls_18 opls_18 C2
! 2023.09.14 2 CR CR CR CR CR CR
2023.09.14 2 CR CR opls_447 opls_447 opls_447 opls_447
2023.09.14 2 CS CS opls_18 opls_18 opls_18 CT
2023.09.14 2 CT CT opls_18 opls_18 opls_18 opls_18
! 2023.09.14 2 CW CW CW CW CW CW
2023.09.14 2 CW CW opls_447 opls_447 opls_447 opls_447
2023.09.14 2 HA HA opls_91 opls_91 opls_91 opls_91
2023.09.14 2 HC HC opls_85 opls_85 opls_85 opls_85
2023.09.14 2 H1 H1 opls_85 opls_85 opls_85 opls_85
2023.09.14 2 NA NA NA NA NA NA


#charges CL&P
Expand All @@ -10820,7 +10924,17 @@
2023.09.13 3 Fbt -0.160
2023.09.13 3 Obt -0.530
2023.09.13 3 Cbt 0.350

2023.09.14 2 C1 -0.17
2023.09.14 2 C2 0.01
2023.09.14 2 CE -0.05
2023.09.14 2 CR -0.11
2023.09.14 2 CS -0.12
2023.09.14 2 CT -0.18
2023.09.14 2 CW -0.13
2023.09.14 2 HA 0.21
! 2023.09.14 2 HC 0.06 same as opls_85
2023.09.14 2 H1 0.13
2023.09.14 2 NA 0.15

#nonbond(12-6) CL&P

Expand All @@ -10845,6 +10959,16 @@
2023.09.13 5 Fbt 3.118 0.25540
2023.09.13 5 Obt 3.150 0.83736
2023.09.13 3 Cbt 3.500 0.27614
2023.09.14 2 C1 3.50 0.27614
2023.09.14 2 C2 3.50 0.27614
2023.09.14 2 CE 3.50 0.27614
2023.09.14 2 CR 3.55 0.29288
2023.09.14 2 CS 3.50 0.27614
2023.09.14 2 CT 3.50 0.27614
2023.09.14 2 CW 3.55 0.29288
2023.09.14 2 HA 2.42 0.12552
2023.09.14 2 H1 2.50 0.12552
2023.09.14 2 NA 3.25 0.71128


#quadratic_bond CL&P
Expand All @@ -10861,6 +10985,11 @@
2023.09.13 3 S O 1.437 5331.0
2023.09.13 3 Sbt Cbt 1.818 1970.0
2023.09.13 3 Cbt Fbt 1.323 3697.0
2023.09.14 2 CR NA 1.315 1996.0
2023.09.14 2 CW NA 1.378 1787.0
2023.09.14 2 CW CW 1.341 2176.0
2023.09.14 2 NA C1 1.466 1410.0


#quadratic_angle CL&P

Expand All @@ -10880,6 +11009,18 @@
2023.09.13 3 N S O 113.6 789.0
2023.09.13 3 Fbt C S 111.8 694.0
2023.09.13 5 Fbt C Fbt 109.1 644.0
2023.09.14 2 CW NA CR 108.0 292.6
2023.09.14 2 CW NA C1 125.6 292.6
2023.09.14 2 CR NA C1 126.4 292.6
2023.09.14 2 NA CR HA 125.1 146.3
2023.09.14 2 NA CR NA 109.8 292.6
2023.09.14 2 NA CW CW 107.1 292.6
2023.09.14 2 NA CW HA 122.0 146.3
2023.09.14 2 CW CW HA 130.9 146.3
! 2023.01.29 1 opls_18 opls_18 opls_18 112.70 58.35 Copied for next
2023.01.29 1 NA opls_18 opls_18 112.70 58.35
!2023.01.29 1 opls_18 opls_18 opls_85 110.70 37.50
2023.01.29 1 NA opls_18 opls_85 110.70 37.50


#simple_fourier_angle CL&P
Expand All @@ -10901,15 +11042,52 @@
> + 1/2*V3*[1 + cos(3*phi3)]
> + 1/2*V4*[1 - cos(4*phi4)]

@units V1 kJ/mol
@units V2 kJ/mol
@units V3 kJ/mol
@units V4 kJ/mol

! Version Ref I J K L V1 V2 V3 V4
!--------- ---- -------- -------- -------- -------- ------ ------- ------ ------
2023.09.13 3 C S N S 32.773 -10.420 -3.915 0.0
2023.09.13 3 C S N S 32.773 -10.420 -3.195 0.0
2023.09.13 3 Fbt C S N 0.0 0.0 1.322 0.0
2023.09.13 3 S N S O 0.0 0.0 -0.015 0.0
2023.09.13 3 Fbt C S O 0.0 0.0 1.451 0.0
2023.09.14 2 * NA CR * 0.0 19.46 0.0 0.0
2023.09.14 2 * CW CW * 0.0 44.98 0.0 0.0
2023.09.14 2 * NA CW * 0.0 12.55 0.0 0.0
2023.09.14 2 CW NA C1 H1 0.0 0.0 0.55 0.0
2023.09.14 2 CR NA C1 H1 0.0 0.0 0.0 0.0
2023.09.14 2 CW NA C1 C2 -5.76 4.43 0.877 0.0
2023.09.14 2 CW NA C1 CE -5.76 4.43 0.877 0.0
2023.09.14 2 CR NA C1 C2 -3.23 0.0 0.0 0.0
2023.09.14 2 CR NA C1 CE -3.23 0.0 0.0 0.0
2023.09.14 2 NA C1 C2 CS 0.738 -0.681 1.02 0.0
2023.09.14 2 NA C1 C2 CT 0.738 -0.681 1.02 0.0
2023.09.14 2 NA C1 C2 opls_85 0.0 0.0 0.0 0.0
2023.09.14 2 NA C1 CE opls_85 0.0 0.0 0.0 0.0

! 2023.09.14 2 C*-C*-C*-H* 0 0 1.531 These do not seem to match OPLS, which they should.
! 2023.09.14 2 H*-C*-C*-H* 0 0 1.331
! 2023.09.14 2 C*-C*-C*-C* 0.728 -0.657 1.167



#improper_opls CL&P

> E = 1/2*V2*[1 - cos(2*phi2)]

> k is the central atom

@units V2 kJ/mol

! Version Ref I J K L V2
!--------- ---- -------- -------- -------- -------- ------
2023.09.14 2 * * NA * 8.37
2023.09.14 2 * * CW * 9.2
2023.09.14 2 * * CR * 9.2



#tabulated_angle CL&P

Expand Down Expand Up @@ -10948,7 +11126,7 @@
}
},
"Nbt": {
"2023.09.213": {
"2023.09.13": {
"smarts": [
"[N:1](~[S](~[O])~[O])~[S](~[O])~[O]",
"[N-1:1](~[S](~[O])~[O])~[S](~[O])~[O]"
Expand All @@ -10958,7 +11136,7 @@
}
},
"Sbt": {
"2023.09.213": {
"2023.09.13": {
"smarts": [
"[N](~[S:1](~[O])~[O])~[S:2](~[O])~[O]",
"[N](~[S:1](~[O])~[O])~[S:2](~[O])~[O]"
Expand All @@ -10968,7 +11146,7 @@
}
},
"Obt": {
"2023.09.213": {
"2023.09.13": {
"smarts": [
"[N](~[S](~[O:1])~[O:2])~[S](~[O:3])~[O:4]",
"[N-1](~[S](~[O:1])~[O:2])~[S](~[O:3])~[O:4]"
Expand All @@ -10978,7 +11156,7 @@
}
},
"Cbt": {
"2023.09.213": {
"2023.09.13": {
"smarts": [
"[N](~[S](~[O])(~[O])[C:1](F)(F)F)~[S](~[O])(~[O])[C:2](F)(F)(F)",
"[N-1](~[S](~[O])(~[O])[C:1](F)(F)F)~[S](~[O])(~[O])[C:2](F)(F)(F)"
Expand All @@ -10988,14 +11166,94 @@
}
},
"Fbt": {
"2023.09.213": {
"2023.09.13": {
"smarts": [
"[N](~[S](~[O])(~[O])C([F:1])([F:2])[F:3])~[S](~[O])(~[O])C([F:4])([F:5])([F:6])",
"[N-1](~[S](~[O])(~[O])C([F:1])([F:2])[F:3])~[S](~[O])(~[O])C([F:4])([F:5])([F:6])"
],
"description": "F in bis(trifluormethanesulfonyl)imide",
"overrides": []
}
},
"NA": {
"2023.09.14": {
"smarts": [
"C[n:1]1cc[n:2](c1)C",
"C[n:1]1cc[n+:2](c1)C"
],
"description": "ring N 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"CR": {
"2023.09.14": {
"smarts": [
"Cn1cc[n]([c:1]1)C",
"Cn1cc[n+]([c:1]1)C"
],
"description": "ring single C 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"CW": {
"2023.09.14": {
"smarts": [
"Cn1[c:1][c:2][n](c1)C",
"Cn1[c:1][c:2][n+](c1)C"
],
"description": "ring pair of C's 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"HA": {
"2023.09.14": {
"smarts": [
"Cn1c([H:1])c([H:2])[n](c1([H:3]))C",
"Cn1c([H:1])c([H:2])[n+](c1([H:3]))C"
],
"description": "ring N 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"C1": {
"2023.09.14": {
"smarts": [
"[C:1]n1cc[n](c1)[C:2]",
"[C:1]n1cc[n+](c1)[C:2]"
],
"description": "alkyl carbon bonded to N 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"H1": {
"2023.09.14": {
"smarts": [
"C([H:1])n1cc[n](c1)C[H:2]",
"C([H:1])n1cc[n+](c1)C[H:2]"
],
"description": "H on alkyl C bonded to N 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"C2": {
"2023.09.14": {
"smarts": [
"C[C:1]Cn1cc[n](c1)C",
"C[C:1]Cn1cc[n+](c1)C"
],
"description": "methylene C 2 from N 1-alkyl-3-methylimidazolium cation",
"overrides": []
}
},
"CE": {
"2023.09.14": {
"smarts": [
"[CH3:1]Cn1cc[n](c1)C",
"[CH3:1]Cn1cc[n+](c1)C"
],
"description": "methyl C 2 from N 1-ethyl-3-methylimidazolium cation",
"overrides": []
}
}
}

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