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add test
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@ajfriedman22
ajfriedman22 committed Sep 18, 2024
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2,055 changes: 2,055 additions & 0 deletions ensemble_md/tests/data/coord_swap/A-B.gro
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158 changes: 158 additions & 0 deletions ensemble_md/tests/data/coord_swap/A-B.itp
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[ moleculetype ]
; Name nrexcl
A2B 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 ss 1 A2B S1 1 -0.116300 32.0600
2 cc 1 A2B C2 2 0.402700 12.0100
3 nd 1 A2B N3 3 -0.636000 14.0100 nd -0.634000 14.0100
4 cd 1 A2B C4 4 0.333200 12.0100 cd 0.332200 12.0100
5 cc 1 A2B C5 5 -0.252400 12.0100 cc -0.251400 12.0100
6 c3 1 A2B C6 6 -0.131400 12.0100 c3 -0.110700 12.0100
7 h4 1 A2B H1 7 0.044100 1.0080 h4 0.043100 1.0080
8 h4 1 A2B H2 8 0.180000 1.0080
9 hc 1 A2B H3 9 0.058700 1.0080 hc 0.057250 1.0080
10 hc 1 A2B H4 10 0.058700 1.0080 hc 0.057250 1.0080
11 hc 1 A2B H17 11 0.058700 1.0080 DUM_hc 0.000000 1.0080
12 DUM_c3 1 A2B DC7 12 0.000000 12.0100 c3 -0.089100 12.0100
13 DUM_hc 1 A2B HV5 13 0.000000 1.0080 hc 0.043000 1.0080
14 DUM_hc 1 A2B HV6 14 0.000000 1.0080 hc 0.043000 1.0080
15 DUM_hc 1 A2B HV7 15 0.000000 1.0080 hc 0.043000 1.0080

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 0.175380 193853.088000 0.175380 193853.088000
1 5 1 0.175380 193853.088000 0.175380 193853.088000
2 3 1 0.131580 351221.696000 0.131580 351221.696000
2 6 1 0.150020 213501.152000 0.150020 213501.152000
3 4 1 0.137130 289474.224000 0.137130 289474.224000
4 5 1 0.137300 323205.632000 0.137300 323205.632000
4 7 1 0.108180 307348.272000 0.108180 307348.272000
5 8 1 0.108090 308544.896000 0.108090 308544.896000
6 9 1 0.109620 288905.200000 0.109620 288905.200000
6 10 1 0.109620 288905.200000 0.109620 288905.200000
6 11 1 0.109620 288905.200000 0.109620 288905.200000
6 12 1 0.153540 191535.152000 0.153540 191535.152000
12 13 1 0.109620 288905.200000 0.109620 288905.200000
12 14 1 0.109620 288905.200000 0.109620 288905.200000
12 15 1 0.109620 288905.200000 0.109620 288905.200000

[ pairs ]
; ai aj funct c0 c1 c2 c3
4 6 1
5 6 1
1 9 1
1 10 1
1 11 1
1 7 1
2 8 1
2 7 1
3 9 1
3 10 1
3 11 1
3 8 1
7 8 1
1 12 1
3 12 1
2 13 1
2 14 1
2 15 1
9 13 1
9 14 1
9 15 1
10 13 1
10 14 1
10 15 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 1 116.440050 583.584320 116.440050 583.584320 ; S1 C2 N3
1 2 6 1 121.350052 522.665280 121.350052 522.665280 ; S1 C2 C6
1 5 4 1 111.550048 557.476160 111.550048 557.476160 ; S1 C5 C4
2 1 5 1 90.360039 854.707520 90.360039 854.707520 ; C2 S1 C5
2 3 4 1 105.370045 730.944800 105.370045 730.944800 ; C2 N3 C4
3 2 6 1 123.870053 548.355040 123.870053 548.355040 ; N3 C2 C6
3 4 5 1 111.580048 597.893600 111.580048 597.893600 ; N3 C4 C5
1 5 8 1 120.150052 352.376480 120.150052 352.376480 ; S1 C5 H2
2 6 9 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H3
2 6 10 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H4
2 6 11 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H17
3 4 7 1 121.200052 403.337600 121.200052 403.337600 ; N3 C4 H1
4 5 8 1 129.110055 367.773600 129.110055 367.773600 ; C4 C5 H2
5 4 7 1 127.640055 369.865600 127.640055 369.865600 ; C5 C4 H1
9 6 10 1 107.730046 299.574400 107.730046 299.574400 ; H3 C6 H4
9 6 11 1 107.730046 299.574400 107.730046 299.574400 ; H3 C6 H17
10 6 11 1 107.730046 299.574400 107.730046 299.574400 ; H4 C6 H17
2 6 12 1 112.960048 505.929280 112.960048 505.929280 ; C2 C6 DC7
6 12 13 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC7 HV5
6 12 14 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC7 HV6
6 12 15 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC7 HV7
12 6 9 1 109.680047 362.083360 109.680047 362.083360 ; DC7 C6 H3
12 6 10 1 109.680047 362.083360 109.680047 362.083360 ; DC7 C6 H4
13 12 14 1 107.730046 299.574400 107.730046 299.574400 ; HV5 DC7 HV6
13 12 15 1 107.730046 299.574400 107.730046 299.574400 ; HV5 DC7 HV7
14 12 15 1 107.730046 299.574400 107.730046 299.574400 ; HV6 DC7 HV7

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
1 2 3 4 1 180.0000771 19.874 2 180.0000771 0 2 ; S1 C2 N3 C4 (AAAA->AAAA)
1 5 4 3 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 N3 (AAAA->AAAA)
2 1 5 4 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 C4 (AAAA->AAAA)
2 3 4 5 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 C5 (AAAA->AAAA)
5 1 2 3 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 N3 (AAAA->AAAA)
4 3 2 6 1 180.0000771 19.874 2 180.0000771 0 2 ; C4 N3 C2 C6 (AAAA->AAAA)
5 1 2 6 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 C6 (AAAA->AAAA)
1 2 3 6 4 180.0000771 4.6024 2 180.0000771 0 2 ; S1 C2 N3 C6 (AAAA->AAAA)
1 2 6 9 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA)
1 2 6 10 1 0 0 3 0 0 3 ; S1 C2 C6 H4 (AAAA->AAAA)
1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H17 (AAAA->AAAD)
1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H17 (AAAA->AAAD)
1 5 4 7 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 H1 (AAAA->AAAA)
2 1 5 8 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 H2 (AAAA->AAAA)
2 3 4 7 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 H1 (AAAA->AAAA)
3 2 6 9 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA)
3 2 6 10 1 0 0 3 0 0 3 ; N3 C2 C6 H4 (AAAA->AAAA)
3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H17 (AAAA->AAAD)
3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H17 (AAAA->AAAD)
3 4 5 8 1 180.0000771 16.736 2 180.0000771 0 2 ; N3 C4 C5 H2 (AAAA->AAAA)
7 4 5 8 1 180.0000771 16.736 2 180.0000771 0 2 ; H1 C4 C5 H2 (AAAA->AAAA)
1 2 3 4 1 180.0000771 0 2 180.0000771 19.874 2 ; S1 C2 N3 C4 (AAAA->AAAA)
1 2 6 12 1 0 0 3 0 0 3 ; S1 C2 C6 DC7 (AAAD->AAAA)
1 2 6 12 1 0 0 3 0 0 3 ; S1 C2 C6 DC7 (AAAD->AAAA)
1 5 4 3 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 N3 (AAAA->AAAA)
2 1 5 4 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 C4 (AAAA->AAAA)
2 3 4 5 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 C5 (AAAA->AAAA)
5 1 2 3 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 N3 (AAAA->AAAA)
3 2 6 12 1 0 0 3 0 0 3 ; N3 C2 C6 DC7 (AAAD->AAAA)
3 2 6 12 1 0 0 3 0 0 3 ; N3 C2 C6 DC7 (AAAD->AAAA)
4 3 2 6 1 180.0000771 0 2 180.0000771 19.874 2 ; C4 N3 C2 C6 (AAAA->AAAA)
5 1 2 6 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 C6 (AAAA->AAAA)
1 2 3 6 4 180.0000771 0 2 180.0000771 4.6024 2 ; S1 C2 N3 C6 (AAAA->AAAA)
1 2 6 9 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA)
1 2 6 10 1 0 0 3 0 0 3 ; S1 C2 C6 H4 (AAAA->AAAA)
1 5 4 7 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 H1 (AAAA->AAAA)
2 1 5 8 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 H2 (AAAA->AAAA)
2 3 4 7 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 H1 (AAAA->AAAA)
2 6 12 13 1 0 0 3 0 0.6508444 3 ; C2 C6 DC7 HV5 (AADD->AAAA)
2 6 12 14 1 0 0 3 0 0.6508444 3 ; C2 C6 DC7 HV6 (AADD->AAAA)
2 6 12 15 1 0 0 3 0 0.6508444 3 ; C2 C6 DC7 HV7 (AADD->AAAA)
3 2 6 9 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA)
3 2 6 10 1 0 0 3 0 0 3 ; N3 C2 C6 H4 (AAAA->AAAA)
3 4 5 8 1 180.0000771 0 2 180.0000771 16.736 2 ; N3 C4 C5 H2 (AAAA->AAAA)
7 4 5 8 1 180.0000771 0 2 180.0000771 16.736 2 ; H1 C4 C5 H2 (AAAA->AAAA)
9 6 12 13 1 0 0 3 0 0.50208 3 ; H3 C6 DC7 HV5 (AADD->AAAA)
9 6 12 14 1 0 0 3 0 0.50208 3 ; H3 C6 DC7 HV6 (AADD->AAAA)
9 6 12 15 1 0 0 3 0 0.50208 3 ; H3 C6 DC7 HV7 (AADD->AAAA)
10 6 12 13 1 0 0 3 0 0.50208 3 ; H4 C6 DC7 HV5 (AADD->AAAA)
10 6 12 14 1 0 0 3 0 0.50208 3 ; H4 C6 DC7 HV6 (AADD->AAAA)
10 6 12 15 1 0 0 3 0 0.50208 3 ; H4 C6 DC7 HV7 (AADD->AAAA)
5 7 4 3 4 180.0000771 0 2 180.0000771 4.6024 2 ; C5 H1 C4 N3 (AAAA->AAAA)
1 5 8 4 4 180.0000771 0 2 180.0000771 4.6024 2 ; S1 C5 H2 C4 (AAAA->AAAA)

#ifdef POSRES
#include "posre.itp"
#endif
32 changes: 32 additions & 0 deletions ensemble_md/tests/data/coord_swap/A-B.top
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[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.83333333

[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
ss 16 32.060000 0.00000000 A 0.35324134 1.1815616
cc 6 12.010000 0.00000000 A 0.33152123 0.4133792
nd 7 14.010000 0.00000000 A 0.33841679 0.3937144
cd 6 12.010000 0.00000000 A 0.33152123 0.4133792
c3 6 12.010000 0.00000000 A 0.33977095 0.4510352
h4 1 1.008000 0.00000000 A 0.25363887 0.0673624
hc 1 1.008000 0.00000000 A 0.2600177 0.0870272
DUM_hc 1 0.000000 0.000000 A 0.000000 0.000000
DUM_c3 6 0.000000 0.000000 A 0.000000 0.000000
Na 11 22.99 0.0000 A 2.43928e-01 3.65846e-02
Cl 17 35.45 0.0000 A 4.47766e-01 1.48913e-01
OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01
HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00

#include "A-B.itp"

#include "water_and_ions.itp"

[ system ]
; Name
Generic title in water

[ molecules ]
; Compound #mols
A2B 1
SOL 679
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