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update tutorial
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‎docs/examples/tutorial_2/A-B.gro‎

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‎docs/examples/tutorial_2/A-B.itp‎

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[ moleculetype ]
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; Name nrexcl
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A2B 3
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[ atoms ]
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; nr type resnr residue atom cgnr charge mass typeB chargeB massB
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1 ss 1 A2B S1 1 -0.116300 32.0600
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2 cc 1 A2B C2 2 0.402700 12.0100
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3 nd 1 A2B N3 3 -0.636000 14.0100 nd -0.634000 14.0100
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4 cd 1 A2B C4 4 0.333200 12.0100 cd 0.332200 12.0100
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5 cc 1 A2B C5 5 -0.252400 12.0100 cc -0.251400 12.0100
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6 c3 1 A2B C6 6 -0.131400 12.0100 c3 -0.110700 12.0100
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7 h4 1 A2B H1 7 0.044100 1.0080 h4 0.043100 1.0080
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8 h4 1 A2B H2 8 0.180000 1.0080
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9 hc 1 A2B H3 9 0.058700 1.0080 hc 0.057250 1.0080
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10 hc 1 A2B H4 10 0.058700 1.0080 hc 0.057250 1.0080
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11 hc 1 A2B H17 11 0.058700 1.0080 DUM_hc 0.000000 1.0080
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12 DUM_c3 1 A2B DC7 12 0.000000 12.0100 c3 -0.089100 12.0100
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13 DUM_hc 1 A2B HV5 13 0.000000 1.0080 hc 0.043000 1.0080
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14 DUM_hc 1 A2B HV6 14 0.000000 1.0080 hc 0.043000 1.0080
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15 DUM_hc 1 A2B HV7 15 0.000000 1.0080 hc 0.043000 1.0080
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[ bonds ]
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; ai aj funct c0 c1 c2 c3
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1 2 1 0.175380 193853.088000 0.175380 193853.088000
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1 5 1 0.175380 193853.088000 0.175380 193853.088000
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2 3 1 0.131580 351221.696000 0.131580 351221.696000
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2 6 1 0.150020 213501.152000 0.150020 213501.152000
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3 4 1 0.137130 289474.224000 0.137130 289474.224000
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4 5 1 0.137300 323205.632000 0.137300 323205.632000
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4 7 1 0.108180 307348.272000 0.108180 307348.272000
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5 8 1 0.108090 308544.896000 0.108090 308544.896000
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6 9 1 0.109620 288905.200000 0.109620 288905.200000
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6 10 1 0.109620 288905.200000 0.109620 288905.200000
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6 11 1 0.109620 288905.200000 0.109620 288905.200000
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6 12 1 0.153540 191535.152000 0.153540 191535.152000
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12 13 1 0.109620 288905.200000 0.109620 288905.200000
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12 14 1 0.109620 288905.200000 0.109620 288905.200000
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12 15 1 0.109620 288905.200000 0.109620 288905.200000
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[ pairs ]
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; ai aj funct c0 c1 c2 c3
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4 6 1
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5 6 1
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1 9 1
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1 10 1
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1 11 1
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1 7 1
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2 8 1
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2 7 1
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3 9 1
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3 10 1
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3 11 1
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3 8 1
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7 8 1
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1 12 1
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3 12 1
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2 13 1
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2 14 1
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2 15 1
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9 13 1
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9 14 1
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9 15 1
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10 13 1
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10 14 1
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10 15 1
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[ angles ]
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; ai aj ak funct c0 c1 c2 c3
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1 2 3 1 116.440050 583.584320 116.440050 583.584320 ; S1 C2 N3
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1 2 6 1 121.350052 522.665280 121.350052 522.665280 ; S1 C2 C6
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1 5 4 1 111.550048 557.476160 111.550048 557.476160 ; S1 C5 C4
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2 1 5 1 90.360039 854.707520 90.360039 854.707520 ; C2 S1 C5
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2 3 4 1 105.370045 730.944800 105.370045 730.944800 ; C2 N3 C4
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3 2 6 1 123.870053 548.355040 123.870053 548.355040 ; N3 C2 C6
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3 4 5 1 111.580048 597.893600 111.580048 597.893600 ; N3 C4 C5
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1 5 8 1 120.150052 352.376480 120.150052 352.376480 ; S1 C5 H2
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2 6 9 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H3
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2 6 10 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H4
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2 6 11 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H17
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3 4 7 1 121.200052 403.337600 121.200052 403.337600 ; N3 C4 H1
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4 5 8 1 129.110055 367.773600 129.110055 367.773600 ; C4 C5 H2
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5 4 7 1 127.640055 369.865600 127.640055 369.865600 ; C5 C4 H1
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9 6 10 1 107.730046 299.574400 107.730046 299.574400 ; H3 C6 H4
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9 6 11 1 107.730046 299.574400 107.730046 299.574400 ; H3 C6 H17
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10 6 11 1 107.730046 299.574400 107.730046 299.574400 ; H4 C6 H17
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2 6 12 1 112.960048 505.929280 112.960048 505.929280 ; C2 C6 DC7
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6 12 13 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC7 HV5
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6 12 14 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC7 HV6
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6 12 15 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC7 HV7
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12 6 9 1 109.680047 362.083360 109.680047 362.083360 ; DC7 C6 H3
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12 6 10 1 109.680047 362.083360 109.680047 362.083360 ; DC7 C6 H4
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13 12 14 1 107.730046 299.574400 107.730046 299.574400 ; HV5 DC7 HV6
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13 12 15 1 107.730046 299.574400 107.730046 299.574400 ; HV5 DC7 HV7
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14 12 15 1 107.730046 299.574400 107.730046 299.574400 ; HV6 DC7 HV7
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[ dihedrals ]
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; ai aj ak al funct c0 c1 c2 c3 c4 c5
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1 2 3 4 1 180.0000771 19.874 2 180.0000771 0 2 ; S1 C2 N3 C4 (AAAA->AAAA)
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1 5 4 3 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 N3 (AAAA->AAAA)
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2 1 5 4 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 C4 (AAAA->AAAA)
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2 3 4 5 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 C5 (AAAA->AAAA)
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5 1 2 3 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 N3 (AAAA->AAAA)
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4 3 2 6 1 180.0000771 19.874 2 180.0000771 0 2 ; C4 N3 C2 C6 (AAAA->AAAA)
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5 1 2 6 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 C6 (AAAA->AAAA)
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1 2 3 6 4 180.0000771 4.6024 2 180.0000771 0 2 ; S1 C2 N3 C6 (AAAA->AAAA)
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1 2 6 9 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA)
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1 2 6 10 1 0 0 3 0 0 3 ; S1 C2 C6 H4 (AAAA->AAAA)
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1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H17 (AAAA->AAAD)
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1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H17 (AAAA->AAAD)
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1 5 4 7 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 H1 (AAAA->AAAA)
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2 1 5 8 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 H2 (AAAA->AAAA)
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2 3 4 7 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 H1 (AAAA->AAAA)
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3 2 6 9 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA)
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3 2 6 10 1 0 0 3 0 0 3 ; N3 C2 C6 H4 (AAAA->AAAA)
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3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H17 (AAAA->AAAD)
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3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H17 (AAAA->AAAD)
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3 4 5 8 1 180.0000771 16.736 2 180.0000771 0 2 ; N3 C4 C5 H2 (AAAA->AAAA)
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7 4 5 8 1 180.0000771 16.736 2 180.0000771 0 2 ; H1 C4 C5 H2 (AAAA->AAAA)
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1 2 3 4 1 180.0000771 0 2 180.0000771 19.874 2 ; S1 C2 N3 C4 (AAAA->AAAA)
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1 2 6 12 1 0 0 3 0 0 3 ; S1 C2 C6 DC7 (AAAD->AAAA)
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1 2 6 12 1 0 0 3 0 0 3 ; S1 C2 C6 DC7 (AAAD->AAAA)
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1 5 4 3 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 N3 (AAAA->AAAA)
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2 1 5 4 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 C4 (AAAA->AAAA)
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2 3 4 5 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 C5 (AAAA->AAAA)
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5 1 2 3 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 N3 (AAAA->AAAA)
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3 2 6 12 1 0 0 3 0 0 3 ; N3 C2 C6 DC7 (AAAD->AAAA)
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3 2 6 12 1 0 0 3 0 0 3 ; N3 C2 C6 DC7 (AAAD->AAAA)
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4 3 2 6 1 180.0000771 0 2 180.0000771 19.874 2 ; C4 N3 C2 C6 (AAAA->AAAA)
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5 1 2 6 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 C6 (AAAA->AAAA)
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1 2 3 6 4 180.0000771 0 2 180.0000771 4.6024 2 ; S1 C2 N3 C6 (AAAA->AAAA)
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1 2 6 9 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA)
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1 2 6 10 1 0 0 3 0 0 3 ; S1 C2 C6 H4 (AAAA->AAAA)
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1 5 4 7 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 H1 (AAAA->AAAA)
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2 1 5 8 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 H2 (AAAA->AAAA)
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2 3 4 7 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 H1 (AAAA->AAAA)
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2 6 12 13 1 0 0 3 0 0.6508444 3 ; C2 C6 DC7 HV5 (AADD->AAAA)
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2 6 12 14 1 0 0 3 0 0.6508444 3 ; C2 C6 DC7 HV6 (AADD->AAAA)
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2 6 12 15 1 0 0 3 0 0.6508444 3 ; C2 C6 DC7 HV7 (AADD->AAAA)
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3 2 6 9 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA)
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3 2 6 10 1 0 0 3 0 0 3 ; N3 C2 C6 H4 (AAAA->AAAA)
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3 4 5 8 1 180.0000771 0 2 180.0000771 16.736 2 ; N3 C4 C5 H2 (AAAA->AAAA)
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7 4 5 8 1 180.0000771 0 2 180.0000771 16.736 2 ; H1 C4 C5 H2 (AAAA->AAAA)
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9 6 12 13 1 0 0 3 0 0.50208 3 ; H3 C6 DC7 HV5 (AADD->AAAA)
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9 6 12 14 1 0 0 3 0 0.50208 3 ; H3 C6 DC7 HV6 (AADD->AAAA)
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9 6 12 15 1 0 0 3 0 0.50208 3 ; H3 C6 DC7 HV7 (AADD->AAAA)
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10 6 12 13 1 0 0 3 0 0.50208 3 ; H4 C6 DC7 HV5 (AADD->AAAA)
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10 6 12 14 1 0 0 3 0 0.50208 3 ; H4 C6 DC7 HV6 (AADD->AAAA)
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10 6 12 15 1 0 0 3 0 0.50208 3 ; H4 C6 DC7 HV7 (AADD->AAAA)
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5 7 4 3 4 180.0000771 0 2 180.0000771 4.6024 2 ; C5 H1 C4 N3 (AAAA->AAAA)
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1 5 8 4 4 180.0000771 0 2 180.0000771 4.6024 2 ; S1 C5 H2 C4 (AAAA->AAAA)
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#ifdef POSRES
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#include "posre.itp"
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#endif

‎docs/examples/tutorial_2/A-B.top‎

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[ defaults ]
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; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
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1 2 yes 0.5 0.83333333
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[ atomtypes ]
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; name at.num mass charge ptype sigma epsilon
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ss 16 32.060000 0.00000000 A 0.35324134 1.1815616
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cc 6 12.010000 0.00000000 A 0.33152123 0.4133792
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nd 7 14.010000 0.00000000 A 0.33841679 0.3937144
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cd 6 12.010000 0.00000000 A 0.33152123 0.4133792
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c3 6 12.010000 0.00000000 A 0.33977095 0.4510352
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h4 1 1.008000 0.00000000 A 0.25363887 0.0673624
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hc 1 1.008000 0.00000000 A 0.2600177 0.0870272
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DUM_hc 1 0.000000 0.000000 A 0.000000 0.000000
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DUM_c3 6 0.000000 0.000000 A 0.000000 0.000000
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Na 11 22.99 0.0000 A 2.43928e-01 3.65846e-02
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Cl 17 35.45 0.0000 A 4.47766e-01 1.48913e-01
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OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01
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HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
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#include "A-B.itp"
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#include "water_and_ions.itp"
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[ system ]
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; Name
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Generic title in water
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[ molecules ]
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; Compound #mols
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A2B 1
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SOL 679

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