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ADD PC and ACN solvents
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Ajay Muralidharan committed Apr 14, 2022
1 parent d5de8f3 commit 08bc692
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14 changes: 7 additions & 7 deletions CLIPS.sh
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Expand Up @@ -6,30 +6,30 @@ Help()
echo " "
echo " Syntax: bash CLIPS.sh -c LI -a TF -f EC -n 1 -T 313 -P LI -N S1 -S O2 -R 2 "
echo " Options: "
echo " c) cation (LI or NA) (default = LI) "
echo " c) cation (LI or NA) (default = LI) "
echo " a) anion (TF or TFSI or BLB) (default = TF) "
echo " f) solvent (EC or SOL) (default is EC = Ethylene carbonate, SOL = water) "
echo " f) solvent (EC or SOL or PC or ACN) (default is EC = Ethylene carbonate) (SOL = water, PC = Propylene carbonate, ACN = Acetonitrile) "
echo " n) OpenMP processes (1 or 2 or 3 ...) "
echo " T) TEMPERATURE (default = 313) "
echo " t) sampling time (default = 10 ns) "
echo " P) cation reference atom for distance measurement (LI or NA) (default = LI) "
echo " N) anion reference atom (S1 for TF/TFSI, CL for Chloride) (default = S1) "
echo " S) solvent reference atom (O2 for EC, OW for water) (default = O2) "
echo " S) solvent reference atom (O2 for EC/PC, OW for water, NZ for ACN) (default = O2) "
echo " R) R_SOL (Confines solvent within sphere around center of ions (default = 2 nm) "
echo " h) print this help "
echo " h) print this help "
echo " "
}

# Defaults
TEMPERATURE=313
Ion1=LI
Ion2=TF
Solv=EC
Solv=EC
NTOMP=1 #OMP THREADS
R_SOL=2 #Solvent barrier
CA1=LI #Solute_reference_Atom
CA2=S1 #Solute_reference_Atom
SA21=C4 #Solvent_reference_Atom
SA21=C4 #Solvent_reference_Atom
time=10 #ns

while getopts c:a:f:n:T:t:P:N:S:R:h flag
Expand Down Expand Up @@ -67,7 +67,7 @@ NSOLV=$(bash NSOLV.sh -f $Solv -n $NTOMP)
echo "NSOLV: $NSOLV";
sleep 1

# Retry function
# Retry function
function fail {
echo $1 >&2
exit 1
Expand Down
44 changes: 44 additions & 0 deletions itp/ACN.itp
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[ moleculetype ]
; Name nrexcl
ACN 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 ACN rtp ACN q 0.0
1 opls_755 1 ACN CT 1 -0.08000000 12.011000 ; qtot -0.080000
2 opls_754 1 ACN CZ 2 0.46000000 12.011000 ; qtot 0.380000
3 opls_759 1 ACN H1 3 0.06000000 1.008000 ; qtot 0.440000
4 opls_759 1 ACN H2 4 0.06000000 1.008000 ; qtot 0.500000
5 opls_759 1 ACN H3 5 0.06000000 1.008000 ; qtot 0.560000
6 opls_753 1 ACN NZ 6 -0.56000000 14.006700 ; qtot 0.000000

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 0.14700 326352.000000
1 3 1 0.10900 284512.000000
1 4 1 0.10900 284512.000000
1 5 1 0.10900 284512.000000
2 6 1 0.11570 543920.000000

[ pairs ]
; ai aj funct c0 c1 c2 c3
3 6 1
4 6 1
5 6 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1 108.5000000 292.880000
2 1 4 1 108.5000000 292.880000
2 1 5 1 108.5000000 292.880000
3 1 4 1 107.8000000 276.144000
3 1 5 1 107.8000000 276.144000
4 1 5 1 107.8000000 276.144000
1 2 6 1 180.0000000 1255.200000

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
3 1 2 6 3 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
4 1 2 6 3 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
5 1 2 6 3 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000

118 changes: 118 additions & 0 deletions itp/PC.itp
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[ moleculetype ]
; Name nrexcl
PC 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 PC rtp PC q -0.0
1 opls_774 1 PC C3 1 -0.00380000 12.011000 ; qtot -0.003800
2 opls_777 1 PC H5 2 0.11067500 1.008000 ; qtot 0.106875
3 opls_777 1 PC H6 3 0.11067500 1.008000 ; qtot 0.217550
4 opls_773 1 PC O1 4 -0.42835500 15.999400 ; qtot -0.210805
5 opls_772 1 PC C4 5 0.99645500 12.011000 ; qtot 0.785650
6 opls_771 1 PC O2 6 -0.60591000 15.999400 ; qtot 0.179740
7 opls_773 1 PC O3 7 -0.39140000 15.999400 ; qtot -0.211660
8 opls_775 1 PC C2 8 0.07904000 12.011000 ; qtot -0.132620
9 opls_778 1 PC H4 9 0.11067500 1.008000 ; qtot -0.021945
10 opls_776 1 PC C1 10 -0.31008000 12.011000 ; qtot -0.332025
11 opls_779 1 PC H1 11 0.11067500 1.008000 ; qtot -0.221350
12 opls_779 1 PC H2 12 0.11067500 1.008000 ; qtot -0.110675
13 opls_779 1 PC H3 13 0.10485000 1.008000 ; qtot -0.005825

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 0.10900 284512.000000
1 3 1 0.10900 284512.000000
1 4 1 0.14100 267776.000000
1 8 1 0.15290 224262.400000
4 5 1 0.13270 179075.200000
5 6 1 0.12290 476976.000000
5 7 1 0.13270 179075.200000
7 8 1 0.14100 267776.000000
8 9 1 0.10900 284512.000000
8 10 1 0.15290 224262.400000
10 11 1 0.10900 284512.000000
10 12 1 0.10900 284512.000000
10 13 1 0.10900 284512.000000

[ pairs ]
; ai aj funct c0 c1 c2 c3
1 6 1
1 11 1
1 12 1
1 13 1
2 5 1
2 7 1
2 9 1
2 10 1
3 5 1
3 7 1
3 9 1
3 10 1
4 9 1
4 10 1
5 9 1
5 10 1
6 8 1
7 11 1
7 12 1
7 13 1
9 11 1
9 12 1
9 13 1
4 7 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1 107.8000000 276.144000
2 1 4 1 109.5000000 292.880000
2 1 8 1 110.7000000 313.800000
3 1 4 1 109.5000000 292.880000
3 1 8 1 110.7000000 313.800000
4 1 8 1 109.5000000 418.400000
1 4 5 1 116.9000000 694.544000
4 5 6 1 123.4000000 694.544000
6 5 7 1 123.4000000 694.544000
5 7 8 1 116.9000000 694.544000
1 8 7 1 109.5000000 418.400000
1 8 9 1 110.7000000 313.800000
1 8 10 1 112.7000000 488.273000
7 8 9 1 109.5000000 292.880000
7 8 10 1 109.5000000 418.400000
9 8 10 1 110.7000000 313.800000
8 10 11 1 110.7000000 313.800000
8 10 12 1 110.7000000 313.800000
8 10 13 1 110.7000000 313.800000
11 10 12 1 107.8000000 276.144000
11 10 13 1 107.8000000 276.144000
12 10 13 1 107.8000000 276.144000

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 4 5 3 0.4142100 1.2426500 0.0000000 -1.6568600 0.0000000 0.0000000
3 1 4 5 3 0.4142100 1.2426500 0.0000000 -1.6568600 0.0000000 0.0000000
8 1 4 5 3 -2.1966000 5.2007100 0.5271900 -3.5313000 0.0000000 0.0000000
2 1 8 7 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
2 1 8 9 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
2 1 8 10 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
3 1 8 7 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
3 1 8 9 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
3 1 8 10 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
4 1 8 7 3 -1.1506000 1.1506000 0.0000000 0.0000000 0.0000000 0.0000000
4 1 8 9 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
4 1 8 10 3 2.8744100 0.5815800 2.0920000 -5.5479900 0.0000000 0.0000000
1 4 5 6 3 20.9200000 0.0000000 -20.9200000 0.0000000 0.0000000 0.0000000
6 5 7 8 3 20.9200000 0.0000000 -20.9200000 0.0000000 0.0000000 0.0000000
5 7 8 1 3 -2.1966000 5.2007100 0.5271900 -3.5313000 0.0000000 0.0000000
5 7 8 9 3 0.4142100 1.2426500 0.0000000 -1.6568600 0.0000000 0.0000000
5 7 8 10 3 -2.1966000 5.2007100 0.5271900 -3.5313000 0.0000000 0.0000000
1 8 10 11 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
1 8 10 12 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
1 8 10 13 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
7 8 10 11 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
7 8 10 12 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
7 8 10 13 3 0.9790500 2.9371600 0.0000000 -3.9162200 0.0000000 0.0000000
9 8 10 11 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
9 8 10 12 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000
9 8 10 13 3 0.6276000 1.8828000 0.0000000 -2.5104000 0.0000000 0.0000000

38 changes: 28 additions & 10 deletions itp/atomtypes.itp
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@@ -1,29 +1,47 @@

[ atomtypes ]
; name bond_type at.num mass charge ptype sigma epsilon

;BLB
BB BB 5 10.810000 0.00000000 A 0.3581 0.3974
OH OH 8 15.999400 0.00000000 A 0.29603 0.8793
CO CO 6 12.011000 0.00000000 A 0.34001 0.3601
CT CT 6 12.011000 0.00000000 A 0.34001 0.458
OC OC 8 15.999400 0.00000000 A 0.29603 0.8793
HC HC 1 1.008000 0.00000000 A 0.26498 0.0657

;SPCE
opls_116 OW 8 15.99940 -0.820 A 3.16557e-01 6.50194e-01
opls_117 HW 1 1.00800 0.410 A 0.00000e+00 0.00000e+00
;EC
opls_774 CT 6 12.011000 0.00000000 A 0.35 0.276144
opls_777 HC 1 1.008000 0.00000000 A 0.242 0.06276
opls_773 OS 8 15.999400 0.00000000 A 0.3 0.71128
opls_772 C 6 12.011000 0.00000000 A 0.375 0.43932
opls_771 O 8 15.999400 0.00000000 A 0.296 0.87864

;EC/PC
opls_774 CT 6 12.011000 0.00000000 A 0.35 0.276144
opls_777 HC 1 1.008000 0.00000000 A 0.242 0.06276
opls_773 OS 8 15.999400 0.00000000 A 0.3 0.71128
opls_772 C 6 12.011000 0.00000000 A 0.375 0.43932
opls_771 O 8 15.999400 0.00000000 A 0.296 0.87864
opls_775 CT 6 12.011000 0.00000000 A 0.35 0.276144
opls_778 HC 1 1.008000 0.00000000 A 0.242 0.06276
opls_776 CT 6 12.011000 0.00000000 A 0.35 0.276144
opls_779 HC 1 1.008000 0.00000000 A 0.242 0.06276

;ACN
opls_755 CT 6 12.011000 -0.08000000 A 0.33 0.276144
opls_754 CZ 6 12.011000 0.46000000 A 0.33 0.276144
opls_759 HC 1 1.008000 0.06000000 A 0.25 0.06276
opls_753 NZ 7 14.006700 -0.56000000 A 0.32 0.71128


;LI Maigret
opls_404 Li+ 3 6.941000 1.00000000 A 0.146 0.799144

;simple ions
opls_407 Na+ 11 22.98977 1.000 A 3.33045e-01 1.15980e-02
opls_400 F- 9 18.99840 -1.000 A 2.73295e-01 3.01248e+00
opls_401 Cl- 17 35.45300 -1.000 A 4.41724e-01 4.92833e-01
opls_402 Br- 35 79.90400 -1.000 A 4.62376e-01 3.76560e-01
opls_403 I- 53 126.90450 -1.000 A 5.40000e-01 2.92880e-01
opls_400 F- 9 18.99840 -1.000 A 2.73295e-01 3.01248e+00
opls_401 Cl- 17 35.45300 -1.000 A 4.41724e-01 4.92833e-01
opls_402 Br- 35 79.90400 -1.000 A 4.62376e-01 3.76560e-01
opls_403 I- 53 126.90450 -1.000 A 5.40000e-01 2.92880e-01

;TFSI
opls_967 F1 6 12.011000 0.24000000 A 0.295 0.22175
opls_966 C5 6 12.011000 0.36000000 A 0.35 0.27614
Expand Down
9 changes: 9 additions & 0 deletions struct/ACN.gro
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GROningen MAchine for Chemical Simulation
6
1ACN CT 1 0.197 0.073 0.072
1ACN CZ 2 0.077 0.141 0.120
1ACN H1 3 0.286 0.133 0.051
1ACN H2 4 0.160 0.026 -0.019
1ACN H3 5 0.225 -0.000 0.148
1ACN NZ 6 -0.022 0.186 0.159
0.30800 0.18600 0.17800
16 changes: 16 additions & 0 deletions struct/PC.gro
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Built with Packmol
13
1PC C3 1 0.205 0.088 0.063
1PC H5 2 0.285 0.018 0.038
1PC H6 3 0.166 0.145 -0.022
1PC O1 4 0.118 0.013 0.142
1PC C4 5 0.063 0.090 0.239
1PC O2 6 -0.032 0.058 0.314
1PC O3 7 0.173 0.154 0.278
1PC C2 8 0.249 0.196 0.167
1PC H4 9 0.227 0.296 0.131
1PC C1 10 0.398 0.193 0.208
1PC H1 11 0.418 0.267 0.286
1PC H2 12 0.453 0.229 0.121
1PC H3 13 0.435 0.091 0.220
0.48500 0.28300 0.33600

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