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Merge pull request #505 from carlocamilloni/main
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regtest case with two prior folders
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@carlocamilloni
carlocamilloni authored Dec 9, 2024
2 parents 690369a + 2c751da commit 310b0d1
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7 changes: 4 additions & 3 deletions test/test_inputs/ttrref/config.yml
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@@ -1,9 +1,10 @@
---
- system: ttrref
- egos: production
- epsilon: 0.33
- train: native_MD,fibril_MD
- inter_epsilon: 0.275
- epsilon: 0.1
- reference: ref_intra,ref_inter
- train: native_MD,fibril_MD,fibril_check
- inter_epsilon: 0.2
- no_header
- symmetry:
- ARG NH1 NH2
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2,528 changes: 2,528 additions & 0 deletions test/test_inputs/ttrref/ref_inter/ffnonbonded.itp
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198 changes: 122 additions & 76 deletions ...st_inputs/ttrref/reference/topol_mego.top → ...st_inputs/ttrref/ref_inter/topol_mego.top
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; Multi-eGO force field version beta.4
; https://github.com/multi-ego/multi-eGO
; Please read and cite:
; Scalone, E. et al. PNAS 119, e2203181119 (2022) 10.1073/pnas.2203181119
; Bacic Toplek, F., Scalone, E. et al. JCTC 20, 459-468 (2024) 10.1021/acs.jctc.3c01182
; Created on the 27-11-2024 01:06
; With the following parameters:
; - system = ttr
; - egos = production
; - reference = reference
; - train = native_MD
; - epsilon = 0.1
; - inter_epsilon = 0.1
; - inter_domain_epsilon = 0.1
; - p_to_learn = 0.9995
; - epsilon_min = 0.07
; - force_split =
; - single_molecule = 1
; - custom_dict =
; - custom_c12 =
; - TTR = 0.1
; - TTR = 0.1
; - TTR = {'TTR': 0.1}
; - symmetry :
; - ARG NH1 NH2
; - ASP OD1 OD2
; - GLU OE1 OE2
; - LEU CD1 CD2
; - PHE CD1 CD2
; - PHE CE1 CE2
; - TYR CD1 CD2
; - TYR CE1 CE2
; - VAL CG1 CG2
; - SER O1 O2
; - symmetry_file =
; - f = 1
; - inter_f = 1
; - inter_domain_f = 1
; - relative_c12d = 0.001
; - explicit_name =
; - regtest =
; - config = inputs/ttr/config.yml
; - root_dir = /Users/carlo/Codes/multi-eGO
; - names = TTR


; Include forcefield parameters
#include "ffnonbonded.itp"

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83 80 85 84 2 0.00000 167.42309

[ pairs ]
; ai aj func c6 c12 ; probability rc_probability source
1 4 1 0.000000e+00 1.312089e-07 ; 1.0 1.0 1-4
1 13 1 0.000000e+00 4.000000e-06 ; 1.0 1.0 1-4
3 12 1 0.000000e+00 2.015656e-07 ; 1.0 1.0 1-4
3 13 1 0.000000e+00 2.389453e-06 ; 1.0 1.0 1-4
4 11 1 0.000000e+00 2.026885e-07 ; 1.0 1.0 1-4
11 15 1 0.000000e+00 3.589263e-06 ; 1.0 1.0 1-4
11 18 1 0.000000e+00 1.299285e-06 ; 1.0 1.0 1-4
13 16 1 0.000000e+00 5.766073e-08 ; 1.0 1.0 1-4
13 17 1 0.000000e+00 2.386346e-07 ; 1.0 1.0 1-4
13 20 1 0.000000e+00 3.002258e-07 ; 1.0 1.0 1-4
15 19 1 0.000000e+00 4.153495e-07 ; 1.0 1.0 1-4
15 20 1 0.000000e+00 4.923747e-06 ; 1.0 1.0 1-4
16 18 1 0.000000e+00 8.907293e-08 ; 1.0 1.0 1-4
17 18 1 0.000000e+00 3.686370e-07 ; 1.0 1.0 1-4
18 22 1 0.000000e+00 3.589263e-06 ; 1.0 1.0 1-4
18 26 1 0.000000e+00 1.299285e-06 ; 1.0 1.0 1-4
20 23 1 0.000000e+00 3.198191e-07 ; 1.0 1.0 1-4
20 24 1 0.000000e+00 2.386346e-07 ; 1.0 1.0 1-4
20 28 1 0.000000e+00 3.002258e-07 ; 1.0 1.0 1-4
22 27 1 0.000000e+00 4.153495e-07 ; 1.0 1.0 1-4
22 28 1 0.000000e+00 4.923747e-06 ; 1.0 1.0 1-4
23 26 1 0.000000e+00 4.940490e-07 ; 1.0 1.0 1-4
24 26 1 0.000000e+00 3.686370e-07 ; 1.0 1.0 1-4
26 30 1 0.000000e+00 1.299682e-06 ; 1.0 1.0 1-4
26 31 1 0.000000e+00 1.299285e-06 ; 1.0 1.0 1-4
28 33 1 0.000000e+00 3.002258e-07 ; 1.0 1.0 1-4
30 32 1 0.000000e+00 1.503992e-07 ; 1.0 1.0 1-4
30 33 1 0.000000e+00 1.782902e-06 ; 1.0 1.0 1-4
31 35 1 0.000000e+00 1.299682e-06 ; 1.0 1.0 1-4
31 36 1 0.000000e+00 1.299285e-06 ; 1.0 1.0 1-4
33 38 1 0.000000e+00 3.002258e-07 ; 1.0 1.0 1-4
35 37 1 0.000000e+00 1.503992e-07 ; 1.0 1.0 1-4
35 38 1 0.000000e+00 1.782902e-06 ; 1.0 1.0 1-4
36 40 1 0.000000e+00 1.741839e-06 ; 1.0 1.0 1-4
36 44 1 0.000000e+00 1.299285e-06 ; 1.0 1.0 1-4
38 41 1 0.000000e+00 6.590245e-07 ; 1.0 1.0 1-4
38 46 1 0.000000e+00 3.002258e-07 ; 1.0 1.0 1-4
40 45 1 0.000000e+00 2.015656e-07 ; 1.0 1.0 1-4
40 46 1 0.000000e+00 2.389453e-06 ; 1.0 1.0 1-4
41 44 1 0.000000e+00 1.018045e-06 ; 1.0 1.0 1-4
44 48 1 0.000000e+00 1.741839e-06 ; 1.0 1.0 1-4
44 52 1 0.000000e+00 1.299285e-06 ; 1.0 1.0 1-4
46 49 1 0.000000e+00 6.590245e-07 ; 1.0 1.0 1-4
46 54 1 0.000000e+00 3.002258e-07 ; 1.0 1.0 1-4
48 53 1 0.000000e+00 2.015656e-07 ; 1.0 1.0 1-4
48 54 1 0.000000e+00 2.389453e-06 ; 1.0 1.0 1-4
49 52 1 0.000000e+00 1.018045e-06 ; 1.0 1.0 1-4
52 56 1 0.000000e+00 1.741839e-06 ; 1.0 1.0 1-4
52 58 1 0.000000e+00 1.299285e-06 ; 1.0 1.0 1-4
54 57 1 0.000000e+00 5.766073e-08 ; 1.0 1.0 1-4
54 60 1 0.000000e+00 3.002258e-07 ; 1.0 1.0 1-4
56 59 1 0.000000e+00 2.015656e-07 ; 1.0 1.0 1-4
56 60 1 0.000000e+00 2.389453e-06 ; 1.0 1.0 1-4
57 58 1 0.000000e+00 8.907293e-08 ; 1.0 1.0 1-4
58 62 1 0.000000e+00 1.531778e-06 ; 1.0 1.0 1-4
58 65 1 0.000000e+00 1.299285e-06 ; 1.0 1.0 1-4
60 63 1 0.000000e+00 2.812498e-07 ; 1.0 1.0 1-4
60 67 1 0.000000e+00 3.002258e-07 ; 1.0 1.0 1-4
62 66 1 0.000000e+00 1.772574e-07 ; 1.0 1.0 1-4
62 67 1 0.000000e+00 2.101292e-06 ; 1.0 1.0 1-4
63 65 1 0.000000e+00 4.344680e-07 ; 1.0 1.0 1-4
65 69 1 0.000000e+00 1.741839e-06 ; 1.0 1.0 1-4
65 77 1 0.000000e+00 1.299285e-06 ; 1.0 1.0 1-4
67 70 1 0.000000e+00 1.312089e-07 ; 1.0 1.0 1-4
67 79 1 0.000000e+00 3.002258e-07 ; 1.0 1.0 1-4
69 78 1 0.000000e+00 2.015656e-07 ; 1.0 1.0 1-4
69 79 1 0.000000e+00 2.389453e-06 ; 1.0 1.0 1-4
70 77 1 0.000000e+00 2.026885e-07 ; 1.0 1.0 1-4
77 81 1 0.000000e+00 1.741839e-06 ; 1.0 1.0 1-4
77 83 1 0.000000e+00 1.299285e-06 ; 1.0 1.0 1-4
79 82 1 0.000000e+00 5.766073e-08 ; 1.0 1.0 1-4
81 84 1 0.000000e+00 1.631652e-07 ; 1.0 1.0 1-4
81 85 1 0.000000e+00 1.631652e-07 ; 1.0 1.0 1-4
82 83 1 0.000000e+00 8.907293e-08 ; 1.0 1.0 1-4
; ai aj func c6 c12 ; probability rc_probability source
1 4 1 0.000000e+00 1.312089e-07 ; 0.840706 0.966814 native_MD
1 13 1 0.000000e+00 3.893189e-06 ; 1.000000 0.999999 native_MD
3 12 1 0.000000e+00 2.015656e-07 ; 1.000000 0.999974 native_MD
3 13 1 0.000000e+00 2.248767e-06 ; 0.999998 1.000000 native_MD
4 11 1 0.000000e+00 8.435774e-08 ; 0.961086 0.874612 native_MD
11 15 1 0.000000e+00 2.526614e-06 ; 1.000000 1.000000 native_MD
11 18 1 0.000000e+00 1.285926e-06 ; 1.000000 1.000000 native_MD
13 16 1 0.000000e+00 5.766073e-08 ; 0.934533 0.871884 native_MD
13 17 1 0.000000e+00 2.386346e-07 ; 0.996733 0.994608 native_MD
13 20 1 0.000000e+00 3.002258e-07 ; 1.000000 0.999996 native_MD
15 19 1 0.000000e+00 4.153495e-07 ; 0.999999 0.999999 native_MD
15 20 1 0.000000e+00 2.673569e-06 ; 1.000000 1.000000 native_MD
16 18 1 0.000000e+00 8.907293e-08 ; 0.819593 0.814933 native_MD
17 18 1 0.000000e+00 3.686370e-07 ; 0.999928 0.998356 native_MD
18 22 1 0.000000e+00 3.280603e-06 ; 0.999996 1.000000 native_MD
18 26 1 0.000000e+00 1.072149e-06 ; 1.000000 1.000000 native_MD
20 23 1 0.000000e+00 3.198191e-07 ; 0.999993 0.999582 native_MD
20 24 1 0.000000e+00 2.386346e-07 ; 0.993005 0.986554 native_MD
20 28 1 0.000000e+00 3.002258e-07 ; 1.000000 0.999999 native_MD
22 27 1 0.000000e+00 4.153495e-07 ; 1.000000 1.000000 native_MD
22 28 1 0.000000e+00 3.519484e-06 ; 0.999997 0.999997 native_MD
23 26 1 0.000000e+00 4.940490e-07 ; 0.999985 0.999930 native_MD
24 26 1 0.000000e+00 3.686370e-07 ; 0.999867 0.999197 native_MD
26 30 1 0.000000e+00 1.299682e-06 ; 1.000000 0.999997 native_MD
26 31 1 0.000000e+00 1.052537e-06 ; 1.000000 0.999999 native_MD
28 33 1 0.000000e+00 3.002258e-07 ; 1.000000 0.999999 native_MD
30 32 1 0.000000e+00 1.503992e-07 ; 0.999986 0.999791 native_MD
30 33 1 0.000000e+00 1.782902e-06 ; 1.000000 0.999999 native_MD
31 35 1 0.000000e+00 1.299682e-06 ; 1.000000 1.000000 native_MD
31 36 1 0.000000e+00 1.040629e-06 ; 1.000000 1.000000 native_MD
33 38 1 0.000000e+00 3.002258e-07 ; 1.000000 0.999995 native_MD
35 37 1 0.000000e+00 1.503992e-07 ; 0.999971 0.999835 native_MD
35 38 1 0.000000e+00 1.782902e-06 ; 0.999994 1.000000 native_MD
36 40 1 0.000000e+00 1.741839e-06 ; 1.000000 1.000000 native_MD
36 44 1 0.000000e+00 1.084920e-06 ; 1.000000 1.000000 native_MD
38 41 1 0.000000e+00 6.590245e-07 ; 1.000000 1.000000 native_MD
38 46 1 0.000000e+00 3.002258e-07 ; 1.000000 0.999993 native_MD
40 45 1 0.000000e+00 2.015656e-07 ; 1.000000 0.999949 native_MD
40 46 1 0.000000e+00 2.211763e-06 ; 0.999999 0.999999 native_MD
41 44 1 0.000000e+00 9.191547e-07 ; 0.999998 1.000000 native_MD
44 48 1 0.000000e+00 1.741839e-06 ; 0.999995 0.999998 native_MD
44 52 1 0.000000e+00 1.203329e-06 ; 1.000000 0.999996 native_MD
46 49 1 0.000000e+00 6.590245e-07 ; 0.999994 1.000000 native_MD
46 54 1 0.000000e+00 3.002258e-07 ; 1.000000 0.999995 native_MD
48 53 1 0.000000e+00 2.015656e-07 ; 1.000000 0.999978 native_MD
48 54 1 0.000000e+00 2.164842e-06 ; 1.000000 0.999999 native_MD
49 52 1 0.000000e+00 1.018045e-06 ; 0.999995 1.000000 native_MD
52 56 1 0.000000e+00 1.741839e-06 ; 0.999993 1.000000 native_MD
52 58 1 0.000000e+00 1.177106e-06 ; 0.999997 1.000000 native_MD
54 57 1 0.000000e+00 5.766073e-08 ; 0.809068 0.779657 native_MD
54 60 1 0.000000e+00 3.002258e-07 ; 0.999994 1.000000 native_MD
56 59 1 0.000000e+00 2.015656e-07 ; 1.000000 0.999994 native_MD
56 60 1 0.000000e+00 1.548162e-06 ; 0.999996 1.000000 native_MD
57 58 1 0.000000e+00 8.907293e-08 ; 0.842845 0.739526 native_MD
58 62 1 0.000000e+00 1.469381e-06 ; 1.000000 1.000000 native_MD
58 65 1 0.000000e+00 1.299285e-06 ; 1.000000 0.999997 native_MD
60 63 1 0.000000e+00 2.268652e-07 ; 0.999997 0.999999 native_MD
60 67 1 0.000000e+00 1.872399e-07 ; 0.999998 0.999988 native_MD
62 66 1 0.000000e+00 1.772574e-07 ; 1.000000 0.999985 native_MD
62 67 1 0.000000e+00 1.797273e-06 ; 1.000000 0.999994 native_MD
63 65 1 0.000000e+00 4.007696e-07 ; 1.000000 1.000000 native_MD
65 69 1 0.000000e+00 1.741839e-06 ; 1.000000 0.999999 native_MD
65 77 1 0.000000e+00 1.049654e-06 ; 0.999989 0.999997 native_MD
67 70 1 0.000000e+00 1.152281e-07 ; 0.865312 0.852182 native_MD
67 79 1 0.000000e+00 3.002258e-07 ; 0.999997 1.000000 native_MD
69 78 1 0.000000e+00 2.015656e-07 ; 0.999997 0.999998 native_MD
69 79 1 0.000000e+00 2.325047e-06 ; 1.000000 0.999996 native_MD
70 77 1 0.000000e+00 1.405082e-07 ; 0.931917 0.920932 native_MD
77 81 1 0.000000e+00 1.741839e-06 ; 0.999997 0.999997 native_MD
77 83 1 0.000000e+00 1.047992e-06 ; 0.999997 0.999999 native_MD
79 82 1 0.000000e+00 5.766073e-08 ; 0.945808 0.773413 native_MD
81 84 1 0.000000e+00 1.631652e-07 ; 0.999860 0.999809 native_MD
81 85 1 0.000000e+00 1.631652e-07 ; 0.999871 0.999819 native_MD
82 83 1 0.000000e+00 8.907293e-08 ; 0.626099 0.789466 native_MD

[ exclusions ]
; ai aj
Expand Down Expand Up @@ -584,7 +630,7 @@ TTR 3
#endif

[ system ]
ttrref
ttr

[ molecules ]
; Compound #mols
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