| [3493da] | 1 | #key value
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| 2 | actionname "help"
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| 3 | add-atom "1"
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| 4 | add-empty-boundary ""
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| 5 | angle-x "0."
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| 6 | angle-x "0"
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| 7 | angle-y "0."
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| 8 | angle-y "0"
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| 9 | angle-z "0 "
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| 10 | angle-z "0."
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| 11 | angle-z "0"
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| 12 | axis "0 0 1"
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| 13 | axis "0 1 0"
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| 14 | axis "1 2 1"
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| 15 | bin-end "10"
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| 16 | bin-end "20"
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| 17 | bin-end "359"
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| 18 | bin-end "359.5"
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| 19 | bin-end "5"
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| 20 | bin-output-file "bin_output-10.csv"
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| 21 | bin-output-file "bin_output-20.csv"
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| 22 | bin-output-file "bin_output-5.csv"
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| 23 | bin-output-file "bin_output.csv"
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| 24 | bin-output-file "emptybox_histogram.dat"
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| 25 | bin-output-file "hydrogenbox_histogram.dat"
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| 26 | bin-output-file "waterbox_histogram.dat"
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| 27 | bin-output-file "waterbox-mirrored_histogram.dat"
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| 28 | bin-start "0"
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| 29 | bin-start "-0.5"
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| 30 | bin-start "10"
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| 31 | bin-start "5"
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| 32 | bin-width "1."
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| 33 | bond-file "bond.dat"
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| 34 | bond-table "table.dat"
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| [f89b45] | 35 | calculate-bounding-box ""
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| [55f299] | 36 | calculate-molar-mass ""
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| [3493da] | 37 | center-in-box "10 0 0 10 0 10"
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| 38 | change-box "10 0 0 10 0 10"
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| 39 | change-element "H"
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| 40 | change-molname "water"
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| 41 | convex-file "convexfile"
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| 42 | copy-molecule "0"
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| [5ab796] | 43 | create-micelle "200"
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| [3493da] | 44 | default-molname "molname"
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| 45 | deltat "0.01"
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| 46 | depth-first-search "2."
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| [5ab796] | 47 | dipole-angular-correlation "H2O"
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| [3493da] | 48 | distance "1.55"
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| 49 | distances "3.1 3.1 3.1"
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| 50 | distances "3.1 3.1 3.1"
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| 51 | distance-to-boundary "1."
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| 52 | distance-to-molecule "1.5"
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| 53 | distance-to-molecule "2.1"
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| 54 | domain-position "0. 0. 0."
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| 55 | domain-position "0 0 0"
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| 56 | domain-position "10. 10. 10."
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| 57 | DoRotate "0"
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| [5ab796] | 58 | DoSaturate "0"
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| [3493da] | 59 | element-db "./"
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| 60 | elements "1"
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| 61 | elements "1 8"
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| 62 | end-step "1"
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| 63 | fastparsing "1"
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| 64 | fill-molecule "filler.xyz"
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| 65 | fill-void "hydrogen.xyz"
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| 66 | fill-void "water.data"
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| 67 | fill-void "water.xyz"
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| 68 | fragment-molecule "./"
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| 69 | id-mapping "1"
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| 70 | input "test.data"
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| 71 | interpolation-steps "9"
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| 72 | keep-fixed-CenterOfMass "0"
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| 73 | load "test.data"
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| 74 | MaxDistance "-1"
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| 75 | MDSteps "1"
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| 76 | molecule-by-id "0"
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| 77 | nonconvex-envelope "25"
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| 78 | nonconvex-file "NonConvexEnvelope"
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| 79 | nonconvex-file "nonconvexfile"
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| 80 | offset "0"
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| 81 | offset "1"
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| 82 | order "2"
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| 83 | output-file "emptybox_values.dat"
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| 84 | output-file "hydrogenbox_values.dat"
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| 85 | output-file "output-10.csv"
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| 86 | output-file "output-20.csv"
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| 87 | output-file "output-5.csv"
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| 88 | output-file "output.csv"
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| 89 | output-file "waterbox-mirrored_values.dat"
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| 90 | output-file "waterbox_values.dat"
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| 91 | output "store.conf"
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| 92 | output "store.data"
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| 93 | output "store.pdb"
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| 94 | output "store.xyz"
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| 95 | output "test.in"
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| [5ab796] | 96 | output-types "xyz"
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| 97 | output-types "xyz mpqc"
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| [3493da] | 98 | parse-tremolo-potentials "argon.potentials"
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| 99 | parse-tremolo-potentials "tensid.potentials"
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| [5ab796] | 100 | parser-parameters "mpqc"
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| 101 | parser-parameters "psi3"
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| [3493da] | 102 | periodic "0"
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| 103 | position "0 0 0"
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| 104 | position "0 0 1"
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| 105 | position "0 0 10"
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| 106 | position "10 10 10"
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| 107 | position "10. 10. 10."
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| 108 | position "1 2 1"
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| 109 | position "5.63 5.71 5.71"
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| 110 | position "7.283585982 3.275186040 3.535886037"
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| 111 | position "9.78 2.64 2.64"
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| [5ab796] | 112 | radius "20."
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| [3493da] | 113 | random-atom-displacement "0."
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| 114 | random-molecule-displacement "0."
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| 115 | random-number-distribution-parameters "max=20;"
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| 116 | random-number-engine-parameters "seed=2;"
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| 117 | repeat-box "1 1 1"
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| 118 | rotate-around-origin "180."
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| 119 | rotate-around-origin "20."
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| 120 | rotate-around-origin "360."
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| 121 | rotate-around-origin "90."
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| 122 | rotate-around-self "180."
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| 123 | rotate-around-self "180"
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| 124 | rotate-around-self "20."
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| 125 | rotate-around-self "360."
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| 126 | rotate-around-self "90."
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| 127 | rotate-to-principal-axis-system ""
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| 128 | save-adjacency "test.adj"
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| 129 | save-bonds "test.bond"
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| 130 | save-selected-atoms "testsave.xyz"
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| 131 | save-selected-molecules "testsave.xyz"
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| 132 | save-temperature "test.ekin"
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| 133 | scale-box "0.5 1. 0.9"
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| 134 | select-atom-by-element "1"
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| 135 | select-atom-by-element "4"
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| 136 | select-atom-by-id "0"
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| 137 | select-atoms-inside-cuboid "10 10 10"
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| 138 | select-atoms-inside-cuboid "2 2 2"
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| 139 | select-atoms-inside-sphere "0.2"
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| 140 | select-atoms-inside-sphere "10"
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| 141 | select-atoms-inside-sphere "7."
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| 142 | select-molecule-by-id "0"
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| 143 | select-molecule-by-id "1"
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| 144 | select-molecule-by-id "4"
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| 145 | select-molecule-by-order "-1"
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| 146 | select-molecule-by-order "1"
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| 147 | select-molecule-by-order "-2"
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| 148 | select-molecule-by-order "2"
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| 149 | select-molecules-by-formula "C2H5(OH)"
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| 150 | select-molecules-by-formula "C6H6"
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| 151 | select-molecules-by-formula "H2O"
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| 152 | select-molecules-by-name "water"
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| [5ab796] | 153 | set-parser-parameters "basis = 4-31G"
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| 154 | set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
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| 155 | set-parser-parameters "maxiter = 499"
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| 156 | set-parser-parameters "theory=CLKS"
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| 157 | set-parser-parameters "wfn=scf"
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| 158 | set-parser-parameters "ref=uhf"
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| [3493da] | 159 | set-output "tremolo"
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| 160 | set-random-number-distribution "uniform_int"
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| 161 | set-random-number-engine "lagged_fibonacci607"
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| 162 | set-tremolo-atomdata "ATOMDATA type id x=3"
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| 163 | set-world-time "10"
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| 164 | skiplines "1"
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| 165 | skiplines "2"
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| 166 | start-step "0"
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| 167 | suspend-in-water "1.0"
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| [5ab796] | 168 | time-step-zero "0"
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| [3493da] | 169 | translate-atoms "1. 0. 0."
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| 170 | unselect-atom-by-element "1"
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| 171 | unselect-atom-by-element "4"
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| 172 | unselect-atom-by-id "0"
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| 173 | unselect-atoms-inside-cuboid "10 10 10"
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| 174 | unselect-atoms-inside-cuboid "2 2 2"
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| 175 | unselect-atoms-inside-sphere "10"
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| 176 | unselect-atoms-inside-sphere "7."
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| 177 | unselect-molecule-by-id "0"
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| 178 | unselect-molecule-by-id "4"
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| 179 | unselect-molecule-by-order "-1"
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| 180 | unselect-molecule-by-order "1"
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| 181 | unselect-molecule-by-order "-2"
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| 182 | unselect-molecule-by-order "2"
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| 183 | unselect-molecules-by-formula "C2H5(OH)"
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| 184 | unselect-molecules-by-formula "C3H8"
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| 185 | unselect-molecules-by-formula "C6H6"
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| 186 | unselect-molecules-by-formula "H2O"
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| 187 | unselect-molecules-by-name "water"
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| 188 | verbose "3"
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| 189 | verlet-integration "forces.dat"
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