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  1. .gitattributes +1 -0
  2. 4AA-huge/README.md +55 -0
  3. 4AA-huge/test/AAEW-traj-arrays.npz +3 -0
  4. 4AA-huge/test/AAEW-traj-state0.pdb +65 -0
  5. 4AA-huge/test/AAEW-traj-time.npy +3 -0
  6. 4AA-huge/test/AEME-traj-arrays.npz +3 -0
  7. 4AA-huge/test/AEME-traj-state0.pdb +63 -0
  8. 4AA-huge/test/AEME-traj-time.npy +3 -0
  9. 4AA-huge/test/AEVI-traj-arrays.npz +3 -0
  10. 4AA-huge/test/AEVI-traj-state0.pdb +66 -0
  11. 4AA-huge/test/AEVI-traj-time.npy +3 -0
  12. 4AA-huge/test/AGAK-2-traj-arrays.npz +3 -0
  13. 4AA-huge/test/AGAK-2-traj-state0.pdb +55 -0
  14. 4AA-huge/test/AGAK-2-traj-time.npy +3 -0
  15. 4AA-huge/test/AGAK-traj-arrays.npz +3 -0
  16. 4AA-huge/test/AGAK-traj-state0.pdb +55 -0
  17. 4AA-huge/test/AGAK-traj-time.npy +3 -0
  18. 4AA-huge/test/ALQY-traj-arrays.npz +3 -0
  19. 4AA-huge/test/ALQY-traj-state0.pdb +73 -0
  20. 4AA-huge/test/ALQY-traj-time.npy +3 -0
  21. 4AA-huge/test/ANFG-traj-arrays.npz +3 -0
  22. 4AA-huge/test/ANFG-traj-state0.pdb +57 -0
  23. 4AA-huge/test/ANFG-traj-time.npy +3 -0
  24. 4AA-huge/test/ANYT-traj-arrays.npz +3 -0
  25. 4AA-huge/test/ANYT-traj-state0.pdb +65 -0
  26. 4AA-huge/test/ANYT-traj-time.npy +3 -0
  27. 4AA-huge/test/AVEK-traj-arrays.npz +3 -0
  28. 4AA-huge/test/AVEK-traj-state0.pdb +69 -0
  29. 4AA-huge/test/AVEK-traj-time.npy +3 -0
  30. 4AA-huge/test/AWKC-traj-arrays.npz +3 -0
  31. 4AA-huge/test/AWKC-traj-state0.pdb +73 -0
  32. 4AA-huge/test/AWKC-traj-time.npy +3 -0
  33. 4AA-huge/test/AYTG-traj-arrays.npz +3 -0
  34. 4AA-huge/test/AYTG-traj-state0.pdb +58 -0
  35. 4AA-huge/test/AYTG-traj-time.npy +3 -0
  36. 4AA-huge/test/CHPR-traj-arrays.npz +3 -0
  37. 4AA-huge/test/CHPR-traj-state0.pdb +72 -0
  38. 4AA-huge/test/CHPR-traj-time.npy +3 -0
  39. 4AA-huge/test/CMST-traj-arrays.npz +3 -0
  40. 4AA-huge/test/CMST-traj-state0.pdb +59 -0
  41. 4AA-huge/test/CMST-traj-time.npy +3 -0
  42. 4AA-huge/test/CMTS-traj-arrays.npz +3 -0
  43. 4AA-huge/test/CMTS-traj-state0.pdb +59 -0
  44. 4AA-huge/test/CMTS-traj-time.npy +3 -0
  45. 4AA-huge/test/CSFQ-traj-arrays.npz +3 -0
  46. 4AA-huge/test/CSFQ-traj-state0.pdb +65 -0
  47. 4AA-huge/test/CSFQ-traj-time.npy +3 -0
  48. 4AA-huge/test/CSGS-traj-arrays.npz +3 -0
  49. 4AA-huge/test/CSGS-traj-state0.pdb +46 -0
  50. 4AA-huge/test/CSGS-traj-time.npy +3 -0
.gitattributes CHANGED
@@ -53,3 +53,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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  *.jpg filter=lfs diff=lfs merge=lfs -text
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  *.jpeg filter=lfs diff=lfs merge=lfs -text
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  *.webp filter=lfs diff=lfs merge=lfs -text
 
 
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  *.jpg filter=lfs diff=lfs merge=lfs -text
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  *.jpeg filter=lfs diff=lfs merge=lfs -text
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  *.webp filter=lfs diff=lfs merge=lfs -text
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+ 4AA-huge/val/LIGY-traj.chk-sim.pickle.gz.old filter=lfs diff=lfs merge=lfs -text
4AA-huge/README.md ADDED
@@ -0,0 +1,55 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # 4AA-huge "Four Amino Acid" data set, tetrapeptides
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+
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+ This folder contains a data set of all-atom molecular dynamics trajectories for
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+ tetrapeptides, i.e. small proteins composed of four amino acids.
5
+ The data set contains mostly validation and test trajectories as it was mostly
6
+ used to validation and test purposes.
7
+ The training trajectories used are usually shorter.
8
+ Each peptide is simulated for 1 micros second using classical molecular dynamics and the
9
+ water is simulated using an implicit water model.
10
+
11
+ For each trajectory two files are available:
12
+
13
+ * `protein-state0.pdb`: contains the topology and initial 3D XYZ coordinates.
14
+ * `protein-arrays.npz`: contains trajectory information.
15
+ * `protein-time.npy`: contains the wall-clock simulation time.
16
+
17
+ ## NPZ Information
18
+
19
+ Each NPZ file contains detailed information for a subset of simulation steps.
20
+ There are T such frames and each NPZ file contains the following arrays:
21
+
22
+ * 'step': `(T,)` array, Md step number.
23
+ * 'energies': `(T,2)` array, each row containing [potential, kinetic] energies
24
+ in kJ/mol.
25
+ * 'positions': `(T,num_atoms,3)` array, positions in nm.
26
+ * 'velocities': `(T,num_atoms,3)` array, velocities in nm/ps.
27
+ * 'forces': `(T,num_atoms,3)` array, forces in kJ/(mol nm).
28
+
29
+
30
+ ## Dataset construction
31
+
32
+ The dataset was constructed in the following way:
33
+
34
+ 1. For all included PDB files, perform a molecular
35
+ dynamics simulation:
36
+
37
+ a.) Use OpenMM with the AMBER14 force field and implicit water (`preset=amber14-implicit`).`
38
+
39
+ b.) Perform an energy minimization (relaxation) from the initial PDB
40
+ configuration.
41
+
42
+ c.) Use a Langevin integrator at temperature T=310K, friction=0.3/ps,
43
+ timestep=0.5fs for 2e6 steps to equilibriate ("burn-in phase").
44
+
45
+ d.) Use a Langevin integrator at temperature T=310K, friction=0.3/ps,
46
+ timestep=0.5fs for 5e5 steps to sample a trajectory ("sample phase").
47
+
48
+ 2. Save trajectory information every 1,000 steps (0.5ps) to an `arrays.npz`
49
+ file.
50
+
51
+
52
+ ## Credit and Authors
53
+
54
+ This dataset was created in Oktober 2022 as part of the Timewarp project
55
+
4AA-huge/test/AAEW-traj-arrays.npz ADDED
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4AA-huge/test/AAEW-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-18
2
+ ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 ALA A 1 2.504 1.310 0.847 1.00 0.00 H
4
+ ATOM 3 H3 ALA A 1 2.632 1.450 -0.980 1.00 0.00 H
5
+ ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
10
+ ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
11
+ ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
12
+ ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
13
+ ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
14
+ ATOM 13 N ALA A 2 6.191 3.839 0.000 1.00 0.00 N
15
+ ATOM 14 H ALA A 2 5.715 4.730 0.000 1.00 0.00 H
16
+ ATOM 15 CA ALA A 2 7.640 3.839 0.000 1.00 0.00 C
17
+ ATOM 16 HA ALA A 2 8.004 3.325 0.890 1.00 0.00 H
18
+ ATOM 17 CB ALA A 2 8.189 3.127 -1.232 1.00 0.00 C
19
+ ATOM 18 HB1 ALA A 2 7.841 3.636 -2.131 1.00 0.00 H
20
+ ATOM 19 HB2 ALA A 2 9.279 3.142 -1.206 1.00 0.00 H
21
+ ATOM 20 HB3 ALA A 2 7.841 2.094 -1.241 1.00 0.00 H
22
+ ATOM 21 C ALA A 2 8.188 5.259 0.000 1.00 0.00 C
23
+ ATOM 22 O ALA A 2 7.425 6.222 0.000 1.00 0.00 O
24
+ ATOM 23 N GLU A 3 9.517 5.386 0.000 1.00 0.00 N
25
+ ATOM 24 H GLU A 3 10.103 4.564 0.000 1.00 0.00 H
26
+ ATOM 25 CA GLU A 3 10.161 6.684 0.000 1.00 0.00 C
27
+ ATOM 26 HA GLU A 3 9.863 7.239 -0.890 1.00 0.00 H
28
+ ATOM 27 CB GLU A 3 9.768 7.492 1.232 1.00 0.00 C
29
+ ATOM 28 HB2 GLU A 3 8.688 7.640 1.241 1.00 0.00 H
30
+ ATOM 29 HB3 GLU A 3 10.068 6.954 2.131 1.00 0.00 H
31
+ ATOM 30 CG GLU A 3 10.458 8.835 1.195 1.00 0.00 C
32
+ ATOM 31 HG2 GLU A 3 11.538 8.688 1.186 1.00 0.00 H
33
+ ATOM 32 HG3 GLU A 3 10.158 9.374 0.296 1.00 0.00 H
34
+ ATOM 33 CD GLU A 3 10.065 9.644 2.429 1.00 0.00 C
35
+ ATOM 34 OE1 GLU A 3 10.786 9.518 3.454 1.00 0.00 O
36
+ ATOM 35 OE2 GLU A 3 9.047 10.381 2.334 1.00 0.00 O
37
+ ATOM 36 C GLU A 3 11.677 6.544 0.000 1.00 0.00 C
38
+ ATOM 37 O GLU A 3 12.200 5.432 0.000 1.00 0.00 O
39
+ ATOM 38 N TRP A 4 12.382 7.677 0.000 1.00 0.00 N
40
+ ATOM 39 H TRP A 4 11.906 8.568 0.000 1.00 0.00 H
41
+ ATOM 40 CA TRP A 4 13.831 7.677 0.000 1.00 0.00 C
42
+ ATOM 41 HA TRP A 4 14.195 7.163 0.890 1.00 0.00 H
43
+ ATOM 42 CB TRP A 4 14.380 6.966 -1.232 1.00 0.00 C
44
+ ATOM 43 HB2 TRP A 4 14.032 5.933 -1.241 1.00 0.00 H
45
+ ATOM 44 HB3 TRP A 4 14.032 7.474 -2.131 1.00 0.00 H
46
+ ATOM 45 CG TRP A 4 15.887 6.914 -1.321 1.00 0.00 C
47
+ ATOM 46 CD1 TRP A 4 16.618 6.353 -2.293 1.00 0.00 C
48
+ ATOM 47 HD1 TRP A 4 16.125 5.867 -3.135 1.00 0.00 H
49
+ ATOM 48 NE1 TRP A 4 17.992 6.551 -1.950 1.00 0.00 N
50
+ ATOM 49 HE1 TRP A 4 18.784 6.238 -2.493 1.00 0.00 H
51
+ ATOM 50 CE2 TRP A 4 18.058 7.206 -0.817 1.00 0.00 C
52
+ ATOM 51 CZ2 TRP A 4 19.204 7.608 -0.120 1.00 0.00 C
53
+ ATOM 52 HZ2 TRP A 4 20.193 7.379 -0.517 1.00 0.00 H
54
+ ATOM 53 CH2 TRP A 4 18.984 8.294 1.069 1.00 0.00 C
55
+ ATOM 54 HH2 TRP A 4 19.830 8.638 1.664 1.00 0.00 H
56
+ ATOM 55 CZ3 TRP A 4 17.731 8.546 1.505 1.00 0.00 C
57
+ ATOM 56 HZ3 TRP A 4 17.578 9.086 2.440 1.00 0.00 H
58
+ ATOM 57 CE3 TRP A 4 16.592 8.131 0.786 1.00 0.00 C
59
+ ATOM 58 HE3 TRP A 4 15.596 8.352 1.168 1.00 0.00 H
60
+ ATOM 59 CD2 TRP A 4 16.814 7.440 -0.412 1.00 0.00 C
61
+ ATOM 60 C TRP A 4 14.379 9.097 0.000 1.00 0.00 C
62
+ ATOM 61 O TRP A 4 13.616 10.060 0.000 1.00 0.00 O
63
+ ATOM 62 OXT TRP A 4 15.656 9.066 0.025 1.00 0.00 O
64
+ TER 63 TRP A 4
65
+ END
4AA-huge/test/AAEW-traj-time.npy ADDED
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4AA-huge/test/AEME-traj-arrays.npz ADDED
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4AA-huge/test/AEME-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-21
2
+ ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 ALA A 1 2.496 1.307 0.838 1.00 0.00 H
4
+ ATOM 3 H3 ALA A 1 2.642 1.448 -0.987 1.00 0.00 H
5
+ ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
10
+ ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
11
+ ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
12
+ ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
13
+ ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
14
+ ATOM 13 N GLU A 2 6.191 3.839 0.000 1.00 0.00 N
15
+ ATOM 14 H GLU A 2 5.715 4.730 0.000 1.00 0.00 H
16
+ ATOM 15 CA GLU A 2 7.640 3.839 0.000 1.00 0.00 C
17
+ ATOM 16 HA GLU A 2 8.004 3.325 0.890 1.00 0.00 H
18
+ ATOM 17 CB GLU A 2 8.189 3.127 -1.232 1.00 0.00 C
19
+ ATOM 18 HB2 GLU A 2 7.841 2.094 -1.241 1.00 0.00 H
20
+ ATOM 19 HB3 GLU A 2 7.841 3.636 -2.131 1.00 0.00 H
21
+ ATOM 20 CG GLU A 2 9.698 3.149 -1.195 1.00 0.00 C
22
+ ATOM 21 HG2 GLU A 2 10.047 4.181 -1.186 1.00 0.00 H
23
+ ATOM 22 HG3 GLU A 2 10.047 2.640 -0.296 1.00 0.00 H
24
+ ATOM 23 CD GLU A 2 10.248 2.436 -2.429 1.00 0.00 C
25
+ ATOM 24 OE1 GLU A 2 10.455 3.138 -3.454 1.00 0.00 O
26
+ ATOM 25 OE2 GLU A 2 10.455 1.197 -2.334 1.00 0.00 O
27
+ ATOM 26 C GLU A 2 8.188 5.259 0.000 1.00 0.00 C
28
+ ATOM 27 O GLU A 2 7.425 6.222 0.000 1.00 0.00 O
29
+ ATOM 28 N MET A 3 9.517 5.386 0.000 1.00 0.00 N
30
+ ATOM 29 H MET A 3 10.103 4.564 0.000 1.00 0.00 H
31
+ ATOM 30 CA MET A 3 10.161 6.684 0.000 1.00 0.00 C
32
+ ATOM 31 HA MET A 3 9.863 7.239 -0.890 1.00 0.00 H
33
+ ATOM 32 CB MET A 3 9.768 7.492 1.232 1.00 0.00 C
34
+ ATOM 33 HB2 MET A 3 8.688 7.640 1.241 1.00 0.00 H
35
+ ATOM 34 HB3 MET A 3 10.068 6.954 2.131 1.00 0.00 H
36
+ ATOM 35 CG MET A 3 10.465 8.848 1.195 1.00 0.00 C
37
+ ATOM 36 HG2 MET A 3 11.545 8.702 1.186 1.00 0.00 H
38
+ ATOM 37 HG3 MET A 3 10.165 9.387 0.296 1.00 0.00 H
39
+ ATOM 38 SD MET A 3 10.008 9.820 2.652 1.00 0.00 S
40
+ ATOM 39 CE MET A 3 10.944 11.302 2.341 1.00 0.00 C
41
+ ATOM 40 HE1 MET A 3 10.625 11.743 1.397 1.00 0.00 H
42
+ ATOM 41 HE2 MET A 3 10.777 12.014 3.149 1.00 0.00 H
43
+ ATOM 42 HE3 MET A 3 12.005 11.057 2.287 1.00 0.00 H
44
+ ATOM 43 C MET A 3 11.677 6.544 0.000 1.00 0.00 C
45
+ ATOM 44 O MET A 3 12.200 5.432 0.000 1.00 0.00 O
46
+ ATOM 45 N GLU A 4 12.382 7.677 0.000 1.00 0.00 N
47
+ ATOM 46 H GLU A 4 11.906 8.568 0.000 1.00 0.00 H
48
+ ATOM 47 CA GLU A 4 13.831 7.677 0.000 1.00 0.00 C
49
+ ATOM 48 HA GLU A 4 14.195 7.163 0.890 1.00 0.00 H
50
+ ATOM 49 CB GLU A 4 14.380 6.966 -1.232 1.00 0.00 C
51
+ ATOM 50 HB2 GLU A 4 14.032 5.933 -1.241 1.00 0.00 H
52
+ ATOM 51 HB3 GLU A 4 14.032 7.474 -2.131 1.00 0.00 H
53
+ ATOM 52 CG GLU A 4 15.889 6.987 -1.195 1.00 0.00 C
54
+ ATOM 53 HG2 GLU A 4 16.238 8.020 -1.186 1.00 0.00 H
55
+ ATOM 54 HG3 GLU A 4 16.238 6.479 -0.296 1.00 0.00 H
56
+ ATOM 55 CD GLU A 4 16.439 6.275 -2.429 1.00 0.00 C
57
+ ATOM 56 OE1 GLU A 4 16.646 6.977 -3.454 1.00 0.00 O
58
+ ATOM 57 OE2 GLU A 4 16.646 5.036 -2.334 1.00 0.00 O
59
+ ATOM 58 C GLU A 4 14.379 9.097 0.000 1.00 0.00 C
60
+ ATOM 59 O GLU A 4 13.616 10.060 0.000 1.00 0.00 O
61
+ ATOM 60 OXT GLU A 4 15.666 9.052 0.048 1.00 0.00 O
62
+ TER 61 GLU A 4
63
+ END
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4AA-huge/test/AEVI-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-19
2
+ ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 ALA A 1 2.477 1.310 0.820 1.00 0.00 H
4
+ ATOM 3 H3 ALA A 1 2.661 1.447 -1.000 1.00 0.00 H
5
+ ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
10
+ ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
11
+ ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
12
+ ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
13
+ ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
14
+ ATOM 13 N GLU A 2 6.191 3.839 0.000 1.00 0.00 N
15
+ ATOM 14 H GLU A 2 5.715 4.730 0.000 1.00 0.00 H
16
+ ATOM 15 CA GLU A 2 7.640 3.839 0.000 1.00 0.00 C
17
+ ATOM 16 HA GLU A 2 8.004 3.325 0.890 1.00 0.00 H
18
+ ATOM 17 CB GLU A 2 8.189 3.127 -1.232 1.00 0.00 C
19
+ ATOM 18 HB2 GLU A 2 7.841 2.094 -1.241 1.00 0.00 H
20
+ ATOM 19 HB3 GLU A 2 7.841 3.636 -2.131 1.00 0.00 H
21
+ ATOM 20 CG GLU A 2 9.698 3.149 -1.195 1.00 0.00 C
22
+ ATOM 21 HG2 GLU A 2 10.047 4.181 -1.186 1.00 0.00 H
23
+ ATOM 22 HG3 GLU A 2 10.047 2.640 -0.296 1.00 0.00 H
24
+ ATOM 23 CD GLU A 2 10.248 2.436 -2.429 1.00 0.00 C
25
+ ATOM 24 OE1 GLU A 2 10.455 3.138 -3.454 1.00 0.00 O
26
+ ATOM 25 OE2 GLU A 2 10.455 1.197 -2.334 1.00 0.00 O
27
+ ATOM 26 C GLU A 2 8.188 5.259 0.000 1.00 0.00 C
28
+ ATOM 27 O GLU A 2 7.425 6.222 0.000 1.00 0.00 O
29
+ ATOM 28 N VAL A 3 9.517 5.386 0.000 1.00 0.00 N
30
+ ATOM 29 H VAL A 3 10.103 4.564 0.000 1.00 0.00 H
31
+ ATOM 30 CA VAL A 3 10.161 6.684 0.000 1.00 0.00 C
32
+ ATOM 31 HA VAL A 3 9.863 7.239 -0.890 1.00 0.00 H
33
+ ATOM 32 CB VAL A 3 9.768 7.492 1.232 1.00 0.00 C
34
+ ATOM 33 HB VAL A 3 8.688 7.640 1.241 1.00 0.00 H
35
+ ATOM 34 CG1 VAL A 3 10.189 6.739 2.490 1.00 0.00 C
36
+ ATOM 35 HG11 VAL A 3 11.269 6.592 2.481 1.00 0.00 H
37
+ ATOM 36 HG12 VAL A 3 9.908 7.316 3.371 1.00 0.00 H
38
+ ATOM 37 HG13 VAL A 3 9.691 5.770 2.517 1.00 0.00 H
39
+ ATOM 38 CG2 VAL A 3 10.465 8.848 1.195 1.00 0.00 C
40
+ ATOM 39 HG21 VAL A 3 10.165 9.387 0.296 1.00 0.00 H
41
+ ATOM 40 HG22 VAL A 3 10.185 9.426 2.075 1.00 0.00 H
42
+ ATOM 41 HG23 VAL A 3 11.545 8.702 1.186 1.00 0.00 H
43
+ ATOM 42 C VAL A 3 11.677 6.544 0.000 1.00 0.00 C
44
+ ATOM 43 O VAL A 3 12.200 5.432 0.000 1.00 0.00 O
45
+ ATOM 44 N ILE A 4 12.382 7.677 0.000 1.00 0.00 N
46
+ ATOM 45 H ILE A 4 11.906 8.568 0.000 1.00 0.00 H
47
+ ATOM 46 CA ILE A 4 13.831 7.677 0.000 1.00 0.00 C
48
+ ATOM 47 HA ILE A 4 14.195 7.163 0.890 1.00 0.00 H
49
+ ATOM 48 CB ILE A 4 14.339 6.958 -1.245 1.00 0.00 C
50
+ ATOM 49 HB ILE A 4 13.976 5.931 -1.246 1.00 0.00 H
51
+ ATOM 50 CG2 ILE A 4 13.831 7.677 -2.490 1.00 0.00 C
52
+ ATOM 51 HG21 ILE A 4 14.194 8.705 -2.491 1.00 0.00 H
53
+ ATOM 52 HG22 ILE A 4 14.194 7.164 -3.381 1.00 0.00 H
54
+ ATOM 53 HG23 ILE A 4 12.741 7.677 -2.491 1.00 0.00 H
55
+ ATOM 54 CG1 ILE A 4 15.864 6.958 -1.245 1.00 0.00 C
56
+ ATOM 55 HG12 ILE A 4 16.228 7.986 -1.245 1.00 0.00 H
57
+ ATOM 56 HG13 ILE A 4 16.228 6.445 -0.355 1.00 0.00 H
58
+ ATOM 57 CD1 ILE A 4 16.373 6.239 -2.490 1.00 0.00 C
59
+ ATOM 58 HD11 ILE A 4 16.010 6.753 -3.381 1.00 0.00 H
60
+ ATOM 59 HD12 ILE A 4 17.463 6.239 -2.491 1.00 0.00 H
61
+ ATOM 60 HD13 ILE A 4 16.010 5.212 -2.491 1.00 0.00 H
62
+ ATOM 61 C ILE A 4 14.379 9.097 0.000 1.00 0.00 C
63
+ ATOM 62 O ILE A 4 13.616 10.060 0.000 1.00 0.00 O
64
+ ATOM 63 OXT ILE A 4 15.666 9.052 0.064 1.00 0.00 O
65
+ TER 64 ILE A 4
66
+ END
4AA-huge/test/AEVI-traj-time.npy ADDED
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4AA-huge/test/AGAK-2-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-21
2
+ ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 ALA A 1 2.649 1.450 -0.992 1.00 0.00 H
4
+ ATOM 3 H3 ALA A 1 2.491 1.309 0.834 1.00 0.00 H
5
+ ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
10
+ ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
11
+ ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
12
+ ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
13
+ ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
14
+ ATOM 13 N GLY A 2 6.191 3.839 0.000 1.00 0.00 N
15
+ ATOM 14 H GLY A 2 5.715 4.730 0.000 1.00 0.00 H
16
+ ATOM 15 CA GLY A 2 7.640 3.839 0.000 1.00 0.00 C
17
+ ATOM 16 HA2 GLY A 2 8.004 3.325 0.890 1.00 0.00 H
18
+ ATOM 17 HA3 GLY A 2 8.004 3.325 -0.890 1.00 0.00 H
19
+ ATOM 18 C GLY A 2 8.171 5.265 0.000 1.00 0.00 C
20
+ ATOM 19 O GLY A 2 7.395 6.219 0.000 1.00 0.00 O
21
+ ATOM 20 N ALA A 3 9.498 5.409 0.000 1.00 0.00 N
22
+ ATOM 21 H ALA A 3 10.094 4.594 0.000 1.00 0.00 H
23
+ ATOM 22 CA ALA A 3 10.126 6.715 0.000 1.00 0.00 C
24
+ ATOM 23 HA ALA A 3 9.821 7.266 -0.890 1.00 0.00 H
25
+ ATOM 24 CB ALA A 3 9.723 7.518 1.232 1.00 0.00 C
26
+ ATOM 25 HB1 ALA A 3 10.030 6.984 2.131 1.00 0.00 H
27
+ ATOM 26 HB2 ALA A 3 10.209 8.493 1.206 1.00 0.00 H
28
+ ATOM 27 HB3 ALA A 3 8.641 7.652 1.241 1.00 0.00 H
29
+ ATOM 28 C ALA A 3 11.643 6.593 0.000 1.00 0.00 C
30
+ ATOM 29 O ALA A 3 12.180 5.487 0.000 1.00 0.00 O
31
+ ATOM 30 N LYS A 4 12.335 7.735 0.000 1.00 0.00 N
32
+ ATOM 31 H LYS A 4 11.848 8.620 0.000 1.00 0.00 H
33
+ ATOM 32 CA LYS A 4 13.784 7.753 0.000 1.00 0.00 C
34
+ ATOM 33 HA LYS A 4 14.154 7.243 0.890 1.00 0.00 H
35
+ ATOM 34 CB LYS A 4 14.341 7.048 -1.232 1.00 0.00 C
36
+ ATOM 35 HB2 LYS A 4 14.006 6.011 -1.241 1.00 0.00 H
37
+ ATOM 36 HB3 LYS A 4 13.987 7.552 -2.131 1.00 0.00 H
38
+ ATOM 37 CG LYS A 4 15.865 7.088 -1.195 1.00 0.00 C
39
+ ATOM 38 HG2 LYS A 4 16.202 8.125 -1.186 1.00 0.00 H
40
+ ATOM 39 HG3 LYS A 4 16.221 6.584 -0.296 1.00 0.00 H
41
+ ATOM 40 CD LYS A 4 16.423 6.384 -2.427 1.00 0.00 C
42
+ ATOM 41 HD2 LYS A 4 16.087 5.347 -2.436 1.00 0.00 H
43
+ ATOM 42 HD3 LYS A 4 16.068 6.888 -3.326 1.00 0.00 H
44
+ ATOM 43 CE LYS A 4 17.947 6.424 -2.389 1.00 0.00 C
45
+ ATOM 44 HE2 LYS A 4 18.283 7.461 -2.380 1.00 0.00 H
46
+ ATOM 45 HE3 LYS A 4 18.302 5.920 -1.491 1.00 0.00 H
47
+ ATOM 46 NZ LYS A 4 18.484 5.745 -3.577 1.00 0.00 N
48
+ ATOM 47 HZ1 LYS A 4 18.156 6.212 -4.410 1.00 0.00 H
49
+ ATOM 48 HZ2 LYS A 4 19.494 5.771 -3.552 1.00 0.00 H
50
+ ATOM 49 HZ3 LYS A 4 18.173 4.784 -3.585 1.00 0.00 H
51
+ ATOM 50 C LYS A 4 14.314 9.179 0.000 1.00 0.00 C
52
+ ATOM 51 O LYS A 4 13.539 10.133 0.000 1.00 0.00 O
53
+ ATOM 52 OXT LYS A 4 15.601 9.146 0.063 1.00 0.00 O
54
+ TER 53 LYS A 4
55
+ END
4AA-huge/test/AGAK-2-traj-time.npy ADDED
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4AA-huge/test/AGAK-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-18
2
+ ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 ALA A 1 2.649 1.450 -0.992 1.00 0.00 H
4
+ ATOM 3 H3 ALA A 1 2.491 1.309 0.834 1.00 0.00 H
5
+ ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
10
+ ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
11
+ ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
12
+ ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
13
+ ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
14
+ ATOM 13 N GLY A 2 6.191 3.839 0.000 1.00 0.00 N
15
+ ATOM 14 H GLY A 2 5.715 4.730 0.000 1.00 0.00 H
16
+ ATOM 15 CA GLY A 2 7.640 3.839 0.000 1.00 0.00 C
17
+ ATOM 16 HA2 GLY A 2 8.004 3.325 0.890 1.00 0.00 H
18
+ ATOM 17 HA3 GLY A 2 8.004 3.325 -0.890 1.00 0.00 H
19
+ ATOM 18 C GLY A 2 8.171 5.265 0.000 1.00 0.00 C
20
+ ATOM 19 O GLY A 2 7.395 6.219 0.000 1.00 0.00 O
21
+ ATOM 20 N ALA A 3 9.498 5.409 0.000 1.00 0.00 N
22
+ ATOM 21 H ALA A 3 10.094 4.594 0.000 1.00 0.00 H
23
+ ATOM 22 CA ALA A 3 10.126 6.715 0.000 1.00 0.00 C
24
+ ATOM 23 HA ALA A 3 9.821 7.266 -0.890 1.00 0.00 H
25
+ ATOM 24 CB ALA A 3 9.723 7.518 1.232 1.00 0.00 C
26
+ ATOM 25 HB1 ALA A 3 10.030 6.984 2.131 1.00 0.00 H
27
+ ATOM 26 HB2 ALA A 3 10.209 8.493 1.206 1.00 0.00 H
28
+ ATOM 27 HB3 ALA A 3 8.641 7.652 1.241 1.00 0.00 H
29
+ ATOM 28 C ALA A 3 11.643 6.593 0.000 1.00 0.00 C
30
+ ATOM 29 O ALA A 3 12.180 5.487 0.000 1.00 0.00 O
31
+ ATOM 30 N LYS A 4 12.335 7.735 0.000 1.00 0.00 N
32
+ ATOM 31 H LYS A 4 11.848 8.620 0.000 1.00 0.00 H
33
+ ATOM 32 CA LYS A 4 13.784 7.753 0.000 1.00 0.00 C
34
+ ATOM 33 HA LYS A 4 14.154 7.243 0.890 1.00 0.00 H
35
+ ATOM 34 CB LYS A 4 14.341 7.048 -1.232 1.00 0.00 C
36
+ ATOM 35 HB2 LYS A 4 14.006 6.011 -1.241 1.00 0.00 H
37
+ ATOM 36 HB3 LYS A 4 13.987 7.552 -2.131 1.00 0.00 H
38
+ ATOM 37 CG LYS A 4 15.865 7.088 -1.195 1.00 0.00 C
39
+ ATOM 38 HG2 LYS A 4 16.202 8.125 -1.186 1.00 0.00 H
40
+ ATOM 39 HG3 LYS A 4 16.221 6.584 -0.296 1.00 0.00 H
41
+ ATOM 40 CD LYS A 4 16.423 6.384 -2.427 1.00 0.00 C
42
+ ATOM 41 HD2 LYS A 4 16.087 5.347 -2.436 1.00 0.00 H
43
+ ATOM 42 HD3 LYS A 4 16.068 6.888 -3.326 1.00 0.00 H
44
+ ATOM 43 CE LYS A 4 17.947 6.424 -2.389 1.00 0.00 C
45
+ ATOM 44 HE2 LYS A 4 18.283 7.461 -2.380 1.00 0.00 H
46
+ ATOM 45 HE3 LYS A 4 18.302 5.920 -1.491 1.00 0.00 H
47
+ ATOM 46 NZ LYS A 4 18.484 5.745 -3.577 1.00 0.00 N
48
+ ATOM 47 HZ1 LYS A 4 18.156 6.212 -4.410 1.00 0.00 H
49
+ ATOM 48 HZ2 LYS A 4 19.494 5.771 -3.552 1.00 0.00 H
50
+ ATOM 49 HZ3 LYS A 4 18.173 4.784 -3.585 1.00 0.00 H
51
+ ATOM 50 C LYS A 4 14.314 9.179 0.000 1.00 0.00 C
52
+ ATOM 51 O LYS A 4 13.539 10.133 0.000 1.00 0.00 O
53
+ ATOM 52 OXT LYS A 4 15.601 9.146 0.063 1.00 0.00 O
54
+ TER 53 LYS A 4
55
+ END
4AA-huge/test/AGAK-traj-time.npy ADDED
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4AA-huge/test/ALQY-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-21
2
+ ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 ALA A 1 2.494 1.311 0.838 1.00 0.00 H
4
+ ATOM 3 H3 ALA A 1 2.641 1.449 -0.987 1.00 0.00 H
5
+ ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
10
+ ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
11
+ ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
12
+ ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
13
+ ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
14
+ ATOM 13 N LEU A 2 6.191 3.839 0.000 1.00 0.00 N
15
+ ATOM 14 H LEU A 2 5.715 4.730 0.000 1.00 0.00 H
16
+ ATOM 15 CA LEU A 2 7.640 3.839 0.000 1.00 0.00 C
17
+ ATOM 16 HA LEU A 2 8.004 3.325 0.890 1.00 0.00 H
18
+ ATOM 17 CB LEU A 2 8.189 3.127 -1.232 1.00 0.00 C
19
+ ATOM 18 HB2 LEU A 2 7.841 2.094 -1.241 1.00 0.00 H
20
+ ATOM 19 HB3 LEU A 2 7.841 3.636 -2.131 1.00 0.00 H
21
+ ATOM 20 CG LEU A 2 9.713 3.149 -1.195 1.00 0.00 C
22
+ ATOM 21 HG LEU A 2 10.062 4.181 -1.186 1.00 0.00 H
23
+ ATOM 22 CD1 LEU A 2 10.201 2.437 0.063 1.00 0.00 C
24
+ ATOM 23 HD11 LEU A 2 9.853 1.404 0.055 1.00 0.00 H
25
+ ATOM 24 HD12 LEU A 2 11.291 2.452 0.090 1.00 0.00 H
26
+ ATOM 25 HD13 LEU A 2 9.809 2.945 0.944 1.00 0.00 H
27
+ ATOM 26 CD2 LEU A 2 10.262 2.438 -2.427 1.00 0.00 C
28
+ ATOM 27 HD21 LEU A 2 9.914 2.946 -3.326 1.00 0.00 H
29
+ ATOM 28 HD22 LEU A 2 11.352 2.453 -2.400 1.00 0.00 H
30
+ ATOM 29 HD23 LEU A 2 9.914 1.405 -2.436 1.00 0.00 H
31
+ ATOM 30 C LEU A 2 8.188 5.259 0.000 1.00 0.00 C
32
+ ATOM 31 O LEU A 2 7.425 6.222 0.000 1.00 0.00 O
33
+ ATOM 32 N GLN A 3 9.517 5.386 0.000 1.00 0.00 N
34
+ ATOM 33 H GLN A 3 10.103 4.564 0.000 1.00 0.00 H
35
+ ATOM 34 CA GLN A 3 10.161 6.684 0.000 1.00 0.00 C
36
+ ATOM 35 HA GLN A 3 9.863 7.239 -0.890 1.00 0.00 H
37
+ ATOM 36 CB GLN A 3 9.768 7.492 1.232 1.00 0.00 C
38
+ ATOM 37 HB2 GLN A 3 8.688 7.640 1.241 1.00 0.00 H
39
+ ATOM 38 HB3 GLN A 3 10.068 6.954 2.131 1.00 0.00 H
40
+ ATOM 39 CG GLN A 3 10.465 8.848 1.195 1.00 0.00 C
41
+ ATOM 40 HG2 GLN A 3 11.545 8.702 1.186 1.00 0.00 H
42
+ ATOM 41 HG3 GLN A 3 10.165 9.387 0.296 1.00 0.00 H
43
+ ATOM 42 CD GLN A 3 10.098 9.687 2.410 1.00 0.00 C
44
+ ATOM 43 OE1 GLN A 3 9.330 9.247 3.263 1.00 0.00 O
45
+ ATOM 44 NE2 GLN A 3 10.650 10.900 2.488 1.00 0.00 N
46
+ ATOM 45 HE21 GLN A 3 10.439 11.498 3.275 1.00 0.00 H
47
+ ATOM 46 HE22 GLN A 3 11.275 11.215 1.760 1.00 0.00 H
48
+ ATOM 47 C GLN A 3 11.677 6.544 0.000 1.00 0.00 C
49
+ ATOM 48 O GLN A 3 12.200 5.432 0.000 1.00 0.00 O
50
+ ATOM 49 N TYR A 4 12.382 7.677 0.000 1.00 0.00 N
51
+ ATOM 50 H TYR A 4 11.906 8.568 0.000 1.00 0.00 H
52
+ ATOM 51 CA TYR A 4 13.831 7.677 0.000 1.00 0.00 C
53
+ ATOM 52 HA TYR A 4 14.195 7.163 0.890 1.00 0.00 H
54
+ ATOM 53 CB TYR A 4 14.380 6.966 -1.232 1.00 0.00 C
55
+ ATOM 54 HB2 TYR A 4 14.032 5.933 -1.241 1.00 0.00 H
56
+ ATOM 55 HB3 TYR A 4 14.032 7.474 -2.131 1.00 0.00 H
57
+ ATOM 56 CG TYR A 4 15.889 6.987 -1.195 1.00 0.00 C
58
+ ATOM 57 CD1 TYR A 4 16.624 6.391 -2.227 1.00 0.00 C
59
+ ATOM 58 HD1 TYR A 4 16.106 5.912 -3.058 1.00 0.00 H
60
+ ATOM 59 CE1 TYR A 4 18.023 6.411 -2.193 1.00 0.00 C
61
+ ATOM 60 HE1 TYR A 4 18.595 5.947 -2.997 1.00 0.00 H
62
+ ATOM 61 CZ TYR A 4 18.688 7.027 -1.126 1.00 0.00 C
63
+ ATOM 62 OH TYR A 4 20.048 7.046 -1.092 1.00 0.00 O
64
+ ATOM 63 HH TYR A 4 20.448 6.610 -1.848 1.00 0.00 H
65
+ ATOM 64 CE2 TYR A 4 17.954 7.623 -0.094 1.00 0.00 C
66
+ ATOM 65 HE2 TYR A 4 18.472 8.103 0.737 1.00 0.00 H
67
+ ATOM 66 CD2 TYR A 4 16.555 7.603 -0.128 1.00 0.00 C
68
+ ATOM 67 HD2 TYR A 4 15.983 8.067 0.676 1.00 0.00 H
69
+ ATOM 68 C TYR A 4 14.379 9.097 0.000 1.00 0.00 C
70
+ ATOM 69 O TYR A 4 13.616 10.060 0.000 1.00 0.00 O
71
+ ATOM 70 OXT TYR A 4 15.661 9.067 0.054 1.00 0.00 O
72
+ TER 71 TYR A 4
73
+ END
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4AA-huge/test/ANFG-traj-arrays.npz ADDED
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4AA-huge/test/ANFG-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-18
2
+ ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 ALA A 1 2.496 1.307 0.838 1.00 0.00 H
4
+ ATOM 3 H3 ALA A 1 2.641 1.455 -0.987 1.00 0.00 H
5
+ ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
10
+ ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
11
+ ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
12
+ ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
13
+ ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
14
+ ATOM 13 N ASN A 2 6.191 3.839 0.000 1.00 0.00 N
15
+ ATOM 14 H ASN A 2 5.715 4.730 0.000 1.00 0.00 H
16
+ ATOM 15 CA ASN A 2 7.640 3.839 0.000 1.00 0.00 C
17
+ ATOM 16 HA ASN A 2 8.004 3.325 0.890 1.00 0.00 H
18
+ ATOM 17 CB ASN A 2 8.189 3.127 -1.232 1.00 0.00 C
19
+ ATOM 18 HB2 ASN A 2 7.841 2.094 -1.241 1.00 0.00 H
20
+ ATOM 19 HB3 ASN A 2 7.841 3.636 -2.131 1.00 0.00 H
21
+ ATOM 20 CG ASN A 2 9.711 3.127 -1.232 1.00 0.00 C
22
+ ATOM 21 OD1 ASN A 2 10.335 3.657 -0.315 1.00 0.00 O
23
+ ATOM 22 ND2 ASN A 2 10.309 2.530 -2.266 1.00 0.00 N
24
+ ATOM 23 HD21 ASN A 2 11.317 2.502 -2.315 1.00 0.00 H
25
+ ATOM 24 HD22 ASN A 2 9.750 2.110 -2.994 1.00 0.00 H
26
+ ATOM 25 C ASN A 2 8.188 5.259 0.000 1.00 0.00 C
27
+ ATOM 26 O ASN A 2 7.425 6.222 0.000 1.00 0.00 O
28
+ ATOM 27 N PHE A 3 9.517 5.386 0.000 1.00 0.00 N
29
+ ATOM 28 H PHE A 3 10.103 4.564 0.000 1.00 0.00 H
30
+ ATOM 29 CA PHE A 3 10.161 6.684 0.000 1.00 0.00 C
31
+ ATOM 30 HA PHE A 3 9.863 7.239 -0.890 1.00 0.00 H
32
+ ATOM 31 CB PHE A 3 9.768 7.492 1.232 1.00 0.00 C
33
+ ATOM 32 HB2 PHE A 3 8.688 7.640 1.241 1.00 0.00 H
34
+ ATOM 33 HB3 PHE A 3 10.068 6.954 2.131 1.00 0.00 H
35
+ ATOM 34 CG PHE A 3 10.392 8.865 1.321 1.00 0.00 C
36
+ ATOM 35 CD1 PHE A 3 10.103 9.696 2.410 1.00 0.00 C
37
+ ATOM 36 HD1 PHE A 3 9.427 9.352 3.193 1.00 0.00 H
38
+ ATOM 37 CE1 PHE A 3 10.681 10.968 2.492 1.00 0.00 C
39
+ ATOM 38 HE1 PHE A 3 10.456 11.615 3.340 1.00 0.00 H
40
+ ATOM 39 CZ PHE A 3 11.549 11.409 1.486 1.00 0.00 C
41
+ ATOM 40 HZ PHE A 3 11.999 12.400 1.550 1.00 0.00 H
42
+ ATOM 41 CE2 PHE A 3 11.838 10.578 0.397 1.00 0.00 C
43
+ ATOM 42 HE2 PHE A 3 12.513 10.921 -0.386 1.00 0.00 H
44
+ ATOM 43 CD2 PHE A 3 11.259 9.306 0.315 1.00 0.00 C
45
+ ATOM 44 HD2 PHE A 3 11.485 8.659 -0.533 1.00 0.00 H
46
+ ATOM 45 C PHE A 3 11.677 6.544 0.000 1.00 0.00 C
47
+ ATOM 46 O PHE A 3 12.200 5.432 0.000 1.00 0.00 O
48
+ ATOM 47 N GLY A 4 12.382 7.677 0.000 1.00 0.00 N
49
+ ATOM 48 H GLY A 4 11.906 8.568 0.000 1.00 0.00 H
50
+ ATOM 49 CA GLY A 4 13.831 7.677 0.000 1.00 0.00 C
51
+ ATOM 50 HA2 GLY A 4 14.195 7.163 0.890 1.00 0.00 H
52
+ ATOM 51 HA3 GLY A 4 14.195 7.163 -0.890 1.00 0.00 H
53
+ ATOM 52 C GLY A 4 14.362 9.104 0.000 1.00 0.00 C
54
+ ATOM 53 O GLY A 4 13.586 10.057 0.000 1.00 0.00 O
55
+ ATOM 54 OXT GLY A 4 15.647 9.043 -0.040 1.00 0.00 O
56
+ TER 55 GLY A 4
57
+ END
4AA-huge/test/ANFG-traj-time.npy ADDED
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4AA-huge/test/ANYT-traj-arrays.npz ADDED
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4AA-huge/test/ANYT-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-21
2
+ ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 ALA A 1 2.495 1.311 0.839 1.00 0.00 H
4
+ ATOM 3 H3 ALA A 1 2.641 1.446 -0.986 1.00 0.00 H
5
+ ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
10
+ ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
11
+ ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
12
+ ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
13
+ ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
14
+ ATOM 13 N ASN A 2 6.191 3.839 0.000 1.00 0.00 N
15
+ ATOM 14 H ASN A 2 5.715 4.730 0.000 1.00 0.00 H
16
+ ATOM 15 CA ASN A 2 7.640 3.839 0.000 1.00 0.00 C
17
+ ATOM 16 HA ASN A 2 8.004 3.325 0.890 1.00 0.00 H
18
+ ATOM 17 CB ASN A 2 8.189 3.127 -1.232 1.00 0.00 C
19
+ ATOM 18 HB2 ASN A 2 7.841 2.094 -1.241 1.00 0.00 H
20
+ ATOM 19 HB3 ASN A 2 7.841 3.636 -2.131 1.00 0.00 H
21
+ ATOM 20 CG ASN A 2 9.711 3.127 -1.232 1.00 0.00 C
22
+ ATOM 21 OD1 ASN A 2 10.335 3.657 -0.315 1.00 0.00 O
23
+ ATOM 22 ND2 ASN A 2 10.309 2.530 -2.266 1.00 0.00 N
24
+ ATOM 23 HD21 ASN A 2 11.317 2.502 -2.315 1.00 0.00 H
25
+ ATOM 24 HD22 ASN A 2 9.750 2.110 -2.994 1.00 0.00 H
26
+ ATOM 25 C ASN A 2 8.188 5.259 0.000 1.00 0.00 C
27
+ ATOM 26 O ASN A 2 7.425 6.222 0.000 1.00 0.00 O
28
+ ATOM 27 N TYR A 3 9.517 5.386 0.000 1.00 0.00 N
29
+ ATOM 28 H TYR A 3 10.103 4.564 0.000 1.00 0.00 H
30
+ ATOM 29 CA TYR A 3 10.161 6.684 0.000 1.00 0.00 C
31
+ ATOM 30 HA TYR A 3 9.863 7.239 -0.890 1.00 0.00 H
32
+ ATOM 31 CB TYR A 3 9.768 7.492 1.232 1.00 0.00 C
33
+ ATOM 32 HB2 TYR A 3 8.688 7.640 1.241 1.00 0.00 H
34
+ ATOM 33 HB3 TYR A 3 10.068 6.954 2.131 1.00 0.00 H
35
+ ATOM 34 CG TYR A 3 10.458 8.835 1.195 1.00 0.00 C
36
+ ATOM 35 CD1 TYR A 3 10.251 9.757 2.227 1.00 0.00 C
37
+ ATOM 36 HD1 TYR A 3 9.591 9.507 3.058 1.00 0.00 H
38
+ ATOM 37 CE1 TYR A 3 10.891 11.002 2.193 1.00 0.00 C
39
+ ATOM 38 HE1 TYR A 3 10.730 11.720 2.997 1.00 0.00 H
40
+ ATOM 39 CZ TYR A 3 11.738 11.324 1.126 1.00 0.00 C
41
+ ATOM 40 OH TYR A 3 12.360 12.533 1.092 1.00 0.00 O
42
+ ATOM 41 HH TYR A 3 12.147 13.086 1.848 1.00 0.00 H
43
+ ATOM 42 CE2 TYR A 3 11.946 10.401 0.094 1.00 0.00 C
44
+ ATOM 43 HE2 TYR A 3 12.606 10.652 -0.737 1.00 0.00 H
45
+ ATOM 44 CD2 TYR A 3 11.306 9.157 0.128 1.00 0.00 C
46
+ ATOM 45 HD2 TYR A 3 11.467 8.439 -0.676 1.00 0.00 H
47
+ ATOM 46 C TYR A 3 11.677 6.544 0.000 1.00 0.00 C
48
+ ATOM 47 O TYR A 3 12.200 5.432 0.000 1.00 0.00 O
49
+ ATOM 48 N THR A 4 12.382 7.677 0.000 1.00 0.00 N
50
+ ATOM 49 H THR A 4 11.906 8.568 0.000 1.00 0.00 H
51
+ ATOM 50 CA THR A 4 13.831 7.677 0.000 1.00 0.00 C
52
+ ATOM 51 HA THR A 4 14.195 7.163 0.890 1.00 0.00 H
53
+ ATOM 52 CB THR A 4 14.380 6.966 -1.232 1.00 0.00 C
54
+ ATOM 53 HB THR A 4 15.470 6.981 -1.206 1.00 0.00 H
55
+ ATOM 54 CG2 THR A 4 13.892 5.521 -1.244 1.00 0.00 C
56
+ ATOM 55 HG21 THR A 4 12.803 5.505 -1.271 1.00 0.00 H
57
+ ATOM 56 HG22 THR A 4 14.284 5.012 -2.125 1.00 0.00 H
58
+ ATOM 57 HG23 THR A 4 14.241 5.012 -0.346 1.00 0.00 H
59
+ ATOM 58 OG1 THR A 4 13.923 7.633 -2.411 1.00 0.00 O
60
+ ATOM 59 HG1 THR A 4 14.268 7.185 -3.187 1.00 0.00 H
61
+ ATOM 60 C THR A 4 14.379 9.097 0.000 1.00 0.00 C
62
+ ATOM 61 O THR A 4 13.616 10.060 0.000 1.00 0.00 O
63
+ ATOM 62 OXT THR A 4 15.668 9.040 -0.005 1.00 0.00 O
64
+ TER 63 THR A 4
65
+ END
4AA-huge/test/ANYT-traj-time.npy ADDED
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4AA-huge/test/AVEK-traj-arrays.npz ADDED
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4AA-huge/test/AVEK-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-21
2
+ ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 ALA A 1 2.498 1.311 0.841 1.00 0.00 H
4
+ ATOM 3 H3 ALA A 1 2.638 1.447 -0.984 1.00 0.00 H
5
+ ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
10
+ ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
11
+ ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
12
+ ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
13
+ ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
14
+ ATOM 13 N VAL A 2 6.191 3.839 0.000 1.00 0.00 N
15
+ ATOM 14 H VAL A 2 5.715 4.730 0.000 1.00 0.00 H
16
+ ATOM 15 CA VAL A 2 7.640 3.839 0.000 1.00 0.00 C
17
+ ATOM 16 HA VAL A 2 8.004 3.325 0.890 1.00 0.00 H
18
+ ATOM 17 CB VAL A 2 8.189 3.127 -1.232 1.00 0.00 C
19
+ ATOM 18 HB VAL A 2 7.841 2.094 -1.241 1.00 0.00 H
20
+ ATOM 19 CG1 VAL A 2 7.701 3.839 -2.490 1.00 0.00 C
21
+ ATOM 20 HG11 VAL A 2 8.050 4.872 -2.481 1.00 0.00 H
22
+ ATOM 21 HG12 VAL A 2 8.093 3.331 -3.371 1.00 0.00 H
23
+ ATOM 22 HG13 VAL A 2 6.612 3.824 -2.517 1.00 0.00 H
24
+ ATOM 23 CG2 VAL A 2 9.713 3.149 -1.195 1.00 0.00 C
25
+ ATOM 24 HG21 VAL A 2 10.062 2.640 -0.296 1.00 0.00 H
26
+ ATOM 25 HG22 VAL A 2 10.106 2.641 -2.075 1.00 0.00 H
27
+ ATOM 26 HG23 VAL A 2 10.062 4.181 -1.186 1.00 0.00 H
28
+ ATOM 27 C VAL A 2 8.188 5.259 0.000 1.00 0.00 C
29
+ ATOM 28 O VAL A 2 7.425 6.222 0.000 1.00 0.00 O
30
+ ATOM 29 N GLU A 3 9.517 5.386 0.000 1.00 0.00 N
31
+ ATOM 30 H GLU A 3 10.103 4.564 0.000 1.00 0.00 H
32
+ ATOM 31 CA GLU A 3 10.161 6.684 0.000 1.00 0.00 C
33
+ ATOM 32 HA GLU A 3 9.863 7.239 -0.890 1.00 0.00 H
34
+ ATOM 33 CB GLU A 3 9.768 7.492 1.232 1.00 0.00 C
35
+ ATOM 34 HB2 GLU A 3 8.688 7.640 1.241 1.00 0.00 H
36
+ ATOM 35 HB3 GLU A 3 10.068 6.954 2.131 1.00 0.00 H
37
+ ATOM 36 CG GLU A 3 10.458 8.835 1.195 1.00 0.00 C
38
+ ATOM 37 HG2 GLU A 3 11.538 8.688 1.186 1.00 0.00 H
39
+ ATOM 38 HG3 GLU A 3 10.158 9.374 0.296 1.00 0.00 H
40
+ ATOM 39 CD GLU A 3 10.065 9.644 2.429 1.00 0.00 C
41
+ ATOM 40 OE1 GLU A 3 10.786 9.518 3.454 1.00 0.00 O
42
+ ATOM 41 OE2 GLU A 3 9.047 10.381 2.334 1.00 0.00 O
43
+ ATOM 42 C GLU A 3 11.677 6.544 0.000 1.00 0.00 C
44
+ ATOM 43 O GLU A 3 12.200 5.432 0.000 1.00 0.00 O
45
+ ATOM 44 N LYS A 4 12.382 7.677 0.000 1.00 0.00 N
46
+ ATOM 45 H LYS A 4 11.906 8.568 0.000 1.00 0.00 H
47
+ ATOM 46 CA LYS A 4 13.831 7.677 0.000 1.00 0.00 C
48
+ ATOM 47 HA LYS A 4 14.195 7.163 0.890 1.00 0.00 H
49
+ ATOM 48 CB LYS A 4 14.380 6.966 -1.232 1.00 0.00 C
50
+ ATOM 49 HB2 LYS A 4 14.032 5.933 -1.241 1.00 0.00 H
51
+ ATOM 50 HB3 LYS A 4 14.032 7.474 -2.131 1.00 0.00 H
52
+ ATOM 51 CG LYS A 4 15.904 6.987 -1.195 1.00 0.00 C
53
+ ATOM 52 HG2 LYS A 4 16.253 8.020 -1.186 1.00 0.00 H
54
+ ATOM 53 HG3 LYS A 4 16.253 6.479 -0.296 1.00 0.00 H
55
+ ATOM 54 CD LYS A 4 16.453 6.276 -2.427 1.00 0.00 C
56
+ ATOM 55 HD2 LYS A 4 16.105 5.243 -2.436 1.00 0.00 H
57
+ ATOM 56 HD3 LYS A 4 16.105 6.785 -3.326 1.00 0.00 H
58
+ ATOM 57 CE LYS A 4 17.978 6.298 -2.389 1.00 0.00 C
59
+ ATOM 58 HE2 LYS A 4 18.327 7.330 -2.380 1.00 0.00 H
60
+ ATOM 59 HE3 LYS A 4 18.327 5.789 -1.491 1.00 0.00 H
61
+ ATOM 60 NZ LYS A 4 18.507 5.612 -3.577 1.00 0.00 N
62
+ ATOM 61 HZ1 LYS A 4 18.184 6.084 -4.410 1.00 0.00 H
63
+ ATOM 62 HZ2 LYS A 4 19.517 5.626 -3.552 1.00 0.00 H
64
+ ATOM 63 HZ3 LYS A 4 18.184 4.655 -3.585 1.00 0.00 H
65
+ ATOM 64 C LYS A 4 14.379 9.097 0.000 1.00 0.00 C
66
+ ATOM 65 O LYS A 4 13.616 10.060 0.000 1.00 0.00 O
67
+ ATOM 66 OXT LYS A 4 15.666 9.052 0.049 1.00 0.00 O
68
+ TER 67 LYS A 4
69
+ END
4AA-huge/test/AVEK-traj-time.npy ADDED
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4AA-huge/test/AWKC-traj-arrays.npz ADDED
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4AA-huge/test/AWKC-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-18
2
+ ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 ALA A 1 2.496 1.320 0.842 1.00 0.00 H
4
+ ATOM 3 H3 ALA A 1 2.642 1.447 -0.987 1.00 0.00 H
5
+ ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
10
+ ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
11
+ ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
12
+ ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
13
+ ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
14
+ ATOM 13 N TRP A 2 6.191 3.839 0.000 1.00 0.00 N
15
+ ATOM 14 H TRP A 2 5.715 4.730 0.000 1.00 0.00 H
16
+ ATOM 15 CA TRP A 2 7.640 3.839 0.000 1.00 0.00 C
17
+ ATOM 16 HA TRP A 2 8.004 3.325 0.890 1.00 0.00 H
18
+ ATOM 17 CB TRP A 2 8.189 3.127 -1.232 1.00 0.00 C
19
+ ATOM 18 HB2 TRP A 2 7.841 2.094 -1.241 1.00 0.00 H
20
+ ATOM 19 HB3 TRP A 2 7.841 3.636 -2.131 1.00 0.00 H
21
+ ATOM 20 CG TRP A 2 9.696 3.076 -1.321 1.00 0.00 C
22
+ ATOM 21 CD1 TRP A 2 10.427 2.515 -2.293 1.00 0.00 C
23
+ ATOM 22 HD1 TRP A 2 9.934 2.029 -3.135 1.00 0.00 H
24
+ ATOM 23 NE1 TRP A 2 11.801 2.713 -1.950 1.00 0.00 N
25
+ ATOM 24 HE1 TRP A 2 12.593 2.399 -2.493 1.00 0.00 H
26
+ ATOM 25 CE2 TRP A 2 11.867 3.367 -0.817 1.00 0.00 C
27
+ ATOM 26 CZ2 TRP A 2 13.013 3.770 -0.120 1.00 0.00 C
28
+ ATOM 27 HZ2 TRP A 2 14.002 3.540 -0.517 1.00 0.00 H
29
+ ATOM 28 CH2 TRP A 2 12.793 4.456 1.069 1.00 0.00 C
30
+ ATOM 29 HH2 TRP A 2 13.639 4.799 1.664 1.00 0.00 H
31
+ ATOM 30 CZ3 TRP A 2 11.540 4.708 1.505 1.00 0.00 C
32
+ ATOM 31 HZ3 TRP A 2 11.387 5.247 2.440 1.00 0.00 H
33
+ ATOM 32 CE3 TRP A 2 10.401 4.292 0.786 1.00 0.00 C
34
+ ATOM 33 HE3 TRP A 2 9.405 4.513 1.168 1.00 0.00 H
35
+ ATOM 34 CD2 TRP A 2 10.623 3.601 -0.412 1.00 0.00 C
36
+ ATOM 35 C TRP A 2 8.188 5.259 0.000 1.00 0.00 C
37
+ ATOM 36 O TRP A 2 7.425 6.222 0.000 1.00 0.00 O
38
+ ATOM 37 N LYS A 3 9.517 5.386 0.000 1.00 0.00 N
39
+ ATOM 38 H LYS A 3 10.103 4.564 0.000 1.00 0.00 H
40
+ ATOM 39 CA LYS A 3 10.161 6.684 0.000 1.00 0.00 C
41
+ ATOM 40 HA LYS A 3 9.863 7.239 -0.890 1.00 0.00 H
42
+ ATOM 41 CB LYS A 3 9.768 7.492 1.232 1.00 0.00 C
43
+ ATOM 42 HB2 LYS A 3 8.688 7.640 1.241 1.00 0.00 H
44
+ ATOM 43 HB3 LYS A 3 10.068 6.954 2.131 1.00 0.00 H
45
+ ATOM 44 CG LYS A 3 10.465 8.848 1.195 1.00 0.00 C
46
+ ATOM 45 HG2 LYS A 3 11.545 8.702 1.186 1.00 0.00 H
47
+ ATOM 46 HG3 LYS A 3 10.165 9.387 0.296 1.00 0.00 H
48
+ ATOM 47 CD LYS A 3 10.072 9.656 2.427 1.00 0.00 C
49
+ ATOM 48 HD2 LYS A 3 8.992 9.803 2.436 1.00 0.00 H
50
+ ATOM 49 HD3 LYS A 3 10.373 9.118 3.326 1.00 0.00 H
51
+ ATOM 50 CE LYS A 3 10.769 11.012 2.389 1.00 0.00 C
52
+ ATOM 51 HE2 LYS A 3 11.849 10.866 2.380 1.00 0.00 H
53
+ ATOM 52 HE3 LYS A 3 10.469 11.551 1.491 1.00 0.00 H
54
+ ATOM 53 NZ LYS A 3 10.390 11.791 3.577 1.00 0.00 N
55
+ ATOM 54 HZ1 LYS A 3 10.669 11.292 4.410 1.00 0.00 H
56
+ ATOM 55 HZ2 LYS A 3 10.852 12.689 3.552 1.00 0.00 H
57
+ ATOM 56 HZ3 LYS A 3 9.390 11.927 3.585 1.00 0.00 H
58
+ ATOM 57 C LYS A 3 11.677 6.544 0.000 1.00 0.00 C
59
+ ATOM 58 O LYS A 3 12.200 5.432 0.000 1.00 0.00 O
60
+ ATOM 59 N CYS A 4 12.382 7.677 0.000 1.00 0.00 N
61
+ ATOM 60 H CYS A 4 11.906 8.568 0.000 1.00 0.00 H
62
+ ATOM 61 CA CYS A 4 13.831 7.677 0.000 1.00 0.00 C
63
+ ATOM 62 HA CYS A 4 14.195 7.163 0.890 1.00 0.00 H
64
+ ATOM 63 CB CYS A 4 14.380 6.966 -1.232 1.00 0.00 C
65
+ ATOM 64 HB2 CYS A 4 14.032 5.933 -1.241 1.00 0.00 H
66
+ ATOM 65 HB3 CYS A 4 14.032 7.474 -2.131 1.00 0.00 H
67
+ ATOM 66 SG CYS A 4 16.183 6.888 -1.366 1.00 0.00 S
68
+ ATOM 67 HG CYS A 4 16.209 6.224 -2.518 1.00 0.00 H
69
+ ATOM 68 C CYS A 4 14.379 9.097 0.000 1.00 0.00 C
70
+ ATOM 69 O CYS A 4 13.616 10.060 0.000 1.00 0.00 O
71
+ ATOM 70 OXT CYS A 4 15.666 9.047 0.027 1.00 0.00 O
72
+ TER 71 CYS A 4
73
+ END
4AA-huge/test/AWKC-traj-time.npy ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:5785e5c2e367b2de4514ddf3d2e6e61687a895f17553f6e57a4d8cf354f278e5
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+ size 136
4AA-huge/test/AYTG-traj-arrays.npz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
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4AA-huge/test/AYTG-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-18
2
+ ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 ALA A 1 2.632 1.445 -0.980 1.00 0.00 H
4
+ ATOM 3 H3 ALA A 1 2.503 1.309 0.846 1.00 0.00 H
5
+ ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
10
+ ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
11
+ ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
12
+ ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
13
+ ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
14
+ ATOM 13 N TYR A 2 6.191 3.839 0.000 1.00 0.00 N
15
+ ATOM 14 H TYR A 2 5.715 4.730 0.000 1.00 0.00 H
16
+ ATOM 15 CA TYR A 2 7.640 3.839 0.000 1.00 0.00 C
17
+ ATOM 16 HA TYR A 2 8.004 3.325 0.890 1.00 0.00 H
18
+ ATOM 17 CB TYR A 2 8.189 3.127 -1.232 1.00 0.00 C
19
+ ATOM 18 HB2 TYR A 2 7.841 2.094 -1.241 1.00 0.00 H
20
+ ATOM 19 HB3 TYR A 2 7.841 3.636 -2.131 1.00 0.00 H
21
+ ATOM 20 CG TYR A 2 9.698 3.149 -1.195 1.00 0.00 C
22
+ ATOM 21 CD1 TYR A 2 10.433 2.553 -2.227 1.00 0.00 C
23
+ ATOM 22 HD1 TYR A 2 9.915 2.073 -3.058 1.00 0.00 H
24
+ ATOM 23 CE1 TYR A 2 11.832 2.573 -2.193 1.00 0.00 C
25
+ ATOM 24 HE1 TYR A 2 12.404 2.109 -2.997 1.00 0.00 H
26
+ ATOM 25 CZ TYR A 2 12.497 3.189 -1.126 1.00 0.00 C
27
+ ATOM 26 OH TYR A 2 13.857 3.208 -1.092 1.00 0.00 O
28
+ ATOM 27 HH TYR A 2 14.257 2.772 -1.848 1.00 0.00 H
29
+ ATOM 28 CE2 TYR A 2 11.763 3.785 -0.094 1.00 0.00 C
30
+ ATOM 29 HE2 TYR A 2 12.281 4.264 0.737 1.00 0.00 H
31
+ ATOM 30 CD2 TYR A 2 10.364 3.765 -0.128 1.00 0.00 C
32
+ ATOM 31 HD2 TYR A 2 9.792 4.229 0.676 1.00 0.00 H
33
+ ATOM 32 C TYR A 2 8.188 5.259 0.000 1.00 0.00 C
34
+ ATOM 33 O TYR A 2 7.425 6.222 0.000 1.00 0.00 O
35
+ ATOM 34 N THR A 3 9.517 5.386 0.000 1.00 0.00 N
36
+ ATOM 35 H THR A 3 10.103 4.564 0.000 1.00 0.00 H
37
+ ATOM 36 CA THR A 3 10.161 6.684 0.000 1.00 0.00 C
38
+ ATOM 37 HA THR A 3 9.863 7.239 -0.890 1.00 0.00 H
39
+ ATOM 38 CB THR A 3 9.768 7.492 1.232 1.00 0.00 C
40
+ ATOM 39 HB THR A 3 10.266 8.462 1.206 1.00 0.00 H
41
+ ATOM 40 CG2 THR A 3 8.257 7.698 1.244 1.00 0.00 C
42
+ ATOM 41 HG21 THR A 3 7.758 6.729 1.271 1.00 0.00 H
43
+ ATOM 42 HG22 THR A 3 7.975 8.276 2.125 1.00 0.00 H
44
+ ATOM 43 HG23 THR A 3 7.956 8.236 0.346 1.00 0.00 H
45
+ ATOM 44 OG1 THR A 3 10.163 6.786 2.411 1.00 0.00 O
46
+ ATOM 45 HG1 THR A 3 9.915 7.295 3.187 1.00 0.00 H
47
+ ATOM 46 C THR A 3 11.677 6.544 0.000 1.00 0.00 C
48
+ ATOM 47 O THR A 3 12.200 5.432 0.000 1.00 0.00 O
49
+ ATOM 48 N GLY A 4 12.382 7.677 0.000 1.00 0.00 N
50
+ ATOM 49 H GLY A 4 11.906 8.568 0.000 1.00 0.00 H
51
+ ATOM 50 CA GLY A 4 13.831 7.677 0.000 1.00 0.00 C
52
+ ATOM 51 HA2 GLY A 4 14.195 7.163 0.890 1.00 0.00 H
53
+ ATOM 52 HA3 GLY A 4 14.195 7.163 -0.890 1.00 0.00 H
54
+ ATOM 53 C GLY A 4 14.362 9.104 0.000 1.00 0.00 C
55
+ ATOM 54 O GLY A 4 13.586 10.057 0.000 1.00 0.00 O
56
+ ATOM 55 OXT GLY A 4 15.647 9.042 -0.001 1.00 0.00 O
57
+ TER 56 GLY A 4
58
+ END
4AA-huge/test/AYTG-traj-time.npy ADDED
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1
+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:5adff7633e7c561d35e64606c385b3237573de383b52968b9132e20426a6af7f
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+ size 136
4AA-huge/test/CHPR-traj-arrays.npz ADDED
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1
+ version https://git-lfs.github.com/spec/v1
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4AA-huge/test/CHPR-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-18
2
+ ATOM 1 N CYS A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 CYS A 1 2.641 1.449 -0.986 1.00 0.00 H
4
+ ATOM 3 H3 CYS A 1 2.497 1.313 0.841 1.00 0.00 H
5
+ ATOM 4 H CYS A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA CYS A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA CYS A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB CYS A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB2 CYS A 1 2.497 3.801 1.241 1.00 0.00 H
10
+ ATOM 9 HB3 CYS A 1 3.877 3.116 2.131 1.00 0.00 H
11
+ ATOM 10 SG CYS A 1 4.310 5.304 1.366 1.00 0.00 S
12
+ ATOM 11 HG CYS A 1 3.725 5.622 2.518 1.00 0.00 H
13
+ ATOM 12 C CYS A 1 5.486 2.705 0.000 1.00 0.00 C
14
+ ATOM 13 O CYS A 1 6.009 1.593 0.000 1.00 0.00 O
15
+ ATOM 14 N HIS A 2 6.191 3.839 0.000 1.00 0.00 N
16
+ ATOM 15 H HIS A 2 5.715 4.730 0.000 1.00 0.00 H
17
+ ATOM 16 CA HIS A 2 7.640 3.839 0.000 1.00 0.00 C
18
+ ATOM 17 HA HIS A 2 8.004 3.325 0.890 1.00 0.00 H
19
+ ATOM 18 CB HIS A 2 8.189 3.127 -1.232 1.00 0.00 C
20
+ ATOM 19 HB2 HIS A 2 7.841 2.094 -1.241 1.00 0.00 H
21
+ ATOM 20 HB3 HIS A 2 7.841 3.636 -2.131 1.00 0.00 H
22
+ ATOM 21 CG HIS A 2 9.696 3.076 -1.321 1.00 0.00 C
23
+ ATOM 22 ND1 HIS A 2 10.350 2.463 -2.383 1.00 0.00 N
24
+ ATOM 23 CE1 HIS A 2 11.650 2.579 -2.183 1.00 0.00 C
25
+ ATOM 24 HE1 HIS A 2 12.352 2.162 -2.905 1.00 0.00 H
26
+ ATOM 25 NE2 HIS A 2 11.852 3.226 -1.062 1.00 0.00 N
27
+ ATOM 26 HE2 HIS A 2 12.759 3.448 -0.677 1.00 0.00 H
28
+ ATOM 27 CD2 HIS A 2 10.662 3.554 -0.492 1.00 0.00 C
29
+ ATOM 28 HD2 HIS A 2 10.641 4.099 0.451 1.00 0.00 H
30
+ ATOM 29 C HIS A 2 8.188 5.259 0.000 1.00 0.00 C
31
+ ATOM 30 O HIS A 2 7.425 6.222 0.000 1.00 0.00 O
32
+ ATOM 31 N PRO A 3 9.517 5.386 0.000 1.00 0.00 N
33
+ ATOM 32 CD PRO A 3 10.402 4.228 0.000 1.00 0.00 C
34
+ ATOM 33 HD2 PRO A 3 10.493 3.840 -1.014 1.00 0.00 H
35
+ ATOM 34 HD3 PRO A 3 9.990 3.455 0.649 1.00 0.00 H
36
+ ATOM 35 CG PRO A 3 11.694 4.785 0.522 1.00 0.00 C
37
+ ATOM 36 HG2 PRO A 3 12.522 4.324 -0.016 1.00 0.00 H
38
+ ATOM 37 HG3 PRO A 3 11.789 4.570 1.586 1.00 0.00 H
39
+ ATOM 38 CB PRO A 3 11.636 6.273 0.276 1.00 0.00 C
40
+ ATOM 39 HB2 PRO A 3 12.257 6.519 -0.586 1.00 0.00 H
41
+ ATOM 40 HB3 PRO A 3 12.011 6.797 1.155 1.00 0.00 H
42
+ ATOM 41 CA PRO A 3 10.162 6.686 0.000 1.00 0.00 C
43
+ ATOM 42 HA PRO A 3 9.895 7.263 0.886 1.00 0.00 H
44
+ ATOM 43 C PRO A 3 9.798 7.477 -1.248 1.00 0.00 C
45
+ ATOM 44 O PRO A 3 8.999 7.022 -2.064 1.00 0.00 O
46
+ ATOM 45 N ARG A 4 10.388 8.665 -1.396 1.00 0.00 N
47
+ ATOM 46 H ARG A 4 11.039 8.997 -0.698 1.00 0.00 H
48
+ ATOM 47 CA ARG A 4 10.125 9.514 -2.541 1.00 0.00 C
49
+ ATOM 48 HA ARG A 4 10.403 8.988 -3.455 1.00 0.00 H
50
+ ATOM 49 CB ARG A 4 8.648 9.884 -2.622 1.00 0.00 C
51
+ ATOM 50 HB2 ARG A 4 8.050 8.978 -2.716 1.00 0.00 H
52
+ ATOM 51 HB3 ARG A 4 8.357 10.419 -1.718 1.00 0.00 H
53
+ ATOM 52 CG ARG A 4 8.413 10.775 -3.838 1.00 0.00 C
54
+ ATOM 53 HG2 ARG A 4 9.011 11.682 -3.745 1.00 0.00 H
55
+ ATOM 54 HG3 ARG A 4 8.704 10.240 -4.742 1.00 0.00 H
56
+ ATOM 55 CD ARG A 4 6.936 11.146 -3.919 1.00 0.00 C
57
+ ATOM 56 HD2 ARG A 4 6.338 10.239 -4.012 1.00 0.00 H
58
+ ATOM 57 HD3 ARG A 4 6.645 11.681 -3.015 1.00 0.00 H
59
+ ATOM 58 NE ARG A 4 6.670 12.012 -5.089 1.00 0.00 N
60
+ ATOM 59 HE ARG A 4 7.443 12.262 -5.689 1.00 0.00 H
61
+ ATOM 60 CZ ARG A 4 5.460 12.476 -5.387 1.00 0.00 C
62
+ ATOM 61 NH1 ARG A 4 4.393 12.190 -4.645 1.00 0.00 N
63
+ ATOM 62 HH11 ARG A 4 4.492 11.603 -3.828 1.00 0.00 H
64
+ ATOM 63 HH12 ARG A 4 3.489 12.560 -4.902 1.00 0.00 H
65
+ ATOM 64 NH2 ARG A 4 5.334 13.247 -6.463 1.00 0.00 N
66
+ ATOM 65 HH21 ARG A 4 6.146 13.462 -7.024 1.00 0.00 H
67
+ ATOM 66 HH22 ARG A 4 4.427 13.614 -6.714 1.00 0.00 H
68
+ ATOM 67 C ARG A 4 10.925 10.806 -2.461 1.00 0.00 C
69
+ ATOM 68 O ARG A 4 11.674 11.018 -1.510 1.00 0.00 O
70
+ ATOM 69 OXT ARG A 4 10.710 11.499 -3.526 1.00 0.00 O
71
+ TER 70 ARG A 4
72
+ END
4AA-huge/test/CHPR-traj-time.npy ADDED
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1
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4AA-huge/test/CMST-traj-arrays.npz ADDED
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4AA-huge/test/CMST-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-18
2
+ ATOM 1 N CYS A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 CYS A 1 2.498 1.313 0.842 1.00 0.00 H
4
+ ATOM 3 H3 CYS A 1 2.641 1.450 -0.987 1.00 0.00 H
5
+ ATOM 4 H CYS A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA CYS A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA CYS A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB CYS A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB2 CYS A 1 2.497 3.801 1.241 1.00 0.00 H
10
+ ATOM 9 HB3 CYS A 1 3.877 3.116 2.131 1.00 0.00 H
11
+ ATOM 10 SG CYS A 1 4.310 5.304 1.366 1.00 0.00 S
12
+ ATOM 11 HG CYS A 1 3.725 5.622 2.518 1.00 0.00 H
13
+ ATOM 12 C CYS A 1 5.486 2.705 0.000 1.00 0.00 C
14
+ ATOM 13 O CYS A 1 6.009 1.593 0.000 1.00 0.00 O
15
+ ATOM 14 N MET A 2 6.191 3.839 0.000 1.00 0.00 N
16
+ ATOM 15 H MET A 2 5.715 4.730 0.000 1.00 0.00 H
17
+ ATOM 16 CA MET A 2 7.640 3.839 0.000 1.00 0.00 C
18
+ ATOM 17 HA MET A 2 8.004 3.325 0.890 1.00 0.00 H
19
+ ATOM 18 CB MET A 2 8.189 3.127 -1.232 1.00 0.00 C
20
+ ATOM 19 HB2 MET A 2 7.841 2.094 -1.241 1.00 0.00 H
21
+ ATOM 20 HB3 MET A 2 7.841 3.636 -2.131 1.00 0.00 H
22
+ ATOM 21 CG MET A 2 9.713 3.149 -1.195 1.00 0.00 C
23
+ ATOM 22 HG2 MET A 2 10.062 4.181 -1.186 1.00 0.00 H
24
+ ATOM 23 HG3 MET A 2 10.062 2.640 -0.296 1.00 0.00 H
25
+ ATOM 24 SD MET A 2 10.381 2.308 -2.652 1.00 0.00 S
26
+ ATOM 25 CE MET A 2 12.124 2.487 -2.341 1.00 0.00 C
27
+ ATOM 26 HE1 MET A 2 12.377 2.005 -1.397 1.00 0.00 H
28
+ ATOM 27 HE2 MET A 2 12.688 2.021 -3.149 1.00 0.00 H
29
+ ATOM 28 HE3 MET A 2 12.377 3.546 -2.287 1.00 0.00 H
30
+ ATOM 29 C MET A 2 8.188 5.259 0.000 1.00 0.00 C
31
+ ATOM 30 O MET A 2 7.425 6.222 0.000 1.00 0.00 O
32
+ ATOM 31 N SER A 3 9.517 5.386 0.000 1.00 0.00 N
33
+ ATOM 32 H SER A 3 10.103 4.564 0.000 1.00 0.00 H
34
+ ATOM 33 CA SER A 3 10.161 6.684 0.000 1.00 0.00 C
35
+ ATOM 34 HA SER A 3 9.863 7.239 -0.890 1.00 0.00 H
36
+ ATOM 35 CB SER A 3 9.768 7.492 1.232 1.00 0.00 C
37
+ ATOM 36 HB2 SER A 3 8.688 7.640 1.241 1.00 0.00 H
38
+ ATOM 37 HB3 SER A 3 10.068 6.954 2.131 1.00 0.00 H
39
+ ATOM 38 OG SER A 3 10.422 8.764 1.197 1.00 0.00 O
40
+ ATOM 39 HG SER A 3 10.174 9.272 1.973 1.00 0.00 H
41
+ ATOM 40 C SER A 3 11.677 6.544 0.000 1.00 0.00 C
42
+ ATOM 41 O SER A 3 12.200 5.432 0.000 1.00 0.00 O
43
+ ATOM 42 N THR A 4 12.382 7.677 0.000 1.00 0.00 N
44
+ ATOM 43 H THR A 4 11.906 8.568 0.000 1.00 0.00 H
45
+ ATOM 44 CA THR A 4 13.831 7.677 0.000 1.00 0.00 C
46
+ ATOM 45 HA THR A 4 14.195 7.163 0.890 1.00 0.00 H
47
+ ATOM 46 CB THR A 4 14.380 6.966 -1.232 1.00 0.00 C
48
+ ATOM 47 HB THR A 4 15.470 6.981 -1.206 1.00 0.00 H
49
+ ATOM 48 CG2 THR A 4 13.892 5.521 -1.244 1.00 0.00 C
50
+ ATOM 49 HG21 THR A 4 12.803 5.505 -1.271 1.00 0.00 H
51
+ ATOM 50 HG22 THR A 4 14.284 5.012 -2.125 1.00 0.00 H
52
+ ATOM 51 HG23 THR A 4 14.241 5.012 -0.346 1.00 0.00 H
53
+ ATOM 52 OG1 THR A 4 13.923 7.633 -2.411 1.00 0.00 O
54
+ ATOM 53 HG1 THR A 4 14.268 7.185 -3.187 1.00 0.00 H
55
+ ATOM 54 C THR A 4 14.379 9.097 0.000 1.00 0.00 C
56
+ ATOM 55 O THR A 4 13.616 10.060 0.000 1.00 0.00 O
57
+ ATOM 56 OXT THR A 4 15.667 9.040 0.033 1.00 0.00 O
58
+ TER 57 THR A 4
59
+ END
4AA-huge/test/CMST-traj-time.npy ADDED
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4AA-huge/test/CMTS-traj-arrays.npz ADDED
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4AA-huge/test/CMTS-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-18
2
+ ATOM 1 N CYS A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 CYS A 1 2.495 1.316 0.840 1.00 0.00 H
4
+ ATOM 3 H3 CYS A 1 2.639 1.452 -0.985 1.00 0.00 H
5
+ ATOM 4 H CYS A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA CYS A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA CYS A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB CYS A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB2 CYS A 1 2.497 3.801 1.241 1.00 0.00 H
10
+ ATOM 9 HB3 CYS A 1 3.877 3.116 2.131 1.00 0.00 H
11
+ ATOM 10 SG CYS A 1 4.310 5.304 1.366 1.00 0.00 S
12
+ ATOM 11 HG CYS A 1 3.725 5.622 2.518 1.00 0.00 H
13
+ ATOM 12 C CYS A 1 5.486 2.705 0.000 1.00 0.00 C
14
+ ATOM 13 O CYS A 1 6.009 1.593 0.000 1.00 0.00 O
15
+ ATOM 14 N MET A 2 6.191 3.839 0.000 1.00 0.00 N
16
+ ATOM 15 H MET A 2 5.715 4.730 0.000 1.00 0.00 H
17
+ ATOM 16 CA MET A 2 7.640 3.839 0.000 1.00 0.00 C
18
+ ATOM 17 HA MET A 2 8.004 3.325 0.890 1.00 0.00 H
19
+ ATOM 18 CB MET A 2 8.189 3.127 -1.232 1.00 0.00 C
20
+ ATOM 19 HB2 MET A 2 7.841 2.094 -1.241 1.00 0.00 H
21
+ ATOM 20 HB3 MET A 2 7.841 3.636 -2.131 1.00 0.00 H
22
+ ATOM 21 CG MET A 2 9.713 3.149 -1.195 1.00 0.00 C
23
+ ATOM 22 HG2 MET A 2 10.062 4.181 -1.186 1.00 0.00 H
24
+ ATOM 23 HG3 MET A 2 10.062 2.640 -0.296 1.00 0.00 H
25
+ ATOM 24 SD MET A 2 10.381 2.308 -2.652 1.00 0.00 S
26
+ ATOM 25 CE MET A 2 12.124 2.487 -2.341 1.00 0.00 C
27
+ ATOM 26 HE1 MET A 2 12.377 2.005 -1.397 1.00 0.00 H
28
+ ATOM 27 HE2 MET A 2 12.688 2.021 -3.149 1.00 0.00 H
29
+ ATOM 28 HE3 MET A 2 12.377 3.546 -2.287 1.00 0.00 H
30
+ ATOM 29 C MET A 2 8.188 5.259 0.000 1.00 0.00 C
31
+ ATOM 30 O MET A 2 7.425 6.222 0.000 1.00 0.00 O
32
+ ATOM 31 N THR A 3 9.517 5.386 0.000 1.00 0.00 N
33
+ ATOM 32 H THR A 3 10.103 4.564 0.000 1.00 0.00 H
34
+ ATOM 33 CA THR A 3 10.161 6.684 0.000 1.00 0.00 C
35
+ ATOM 34 HA THR A 3 9.863 7.239 -0.890 1.00 0.00 H
36
+ ATOM 35 CB THR A 3 9.768 7.492 1.232 1.00 0.00 C
37
+ ATOM 36 HB THR A 3 10.266 8.462 1.206 1.00 0.00 H
38
+ ATOM 37 CG2 THR A 3 8.257 7.698 1.244 1.00 0.00 C
39
+ ATOM 38 HG21 THR A 3 7.758 6.729 1.271 1.00 0.00 H
40
+ ATOM 39 HG22 THR A 3 7.975 8.276 2.125 1.00 0.00 H
41
+ ATOM 40 HG23 THR A 3 7.956 8.236 0.346 1.00 0.00 H
42
+ ATOM 41 OG1 THR A 3 10.163 6.786 2.411 1.00 0.00 O
43
+ ATOM 42 HG1 THR A 3 9.915 7.295 3.187 1.00 0.00 H
44
+ ATOM 43 C THR A 3 11.677 6.544 0.000 1.00 0.00 C
45
+ ATOM 44 O THR A 3 12.200 5.432 0.000 1.00 0.00 O
46
+ ATOM 45 N SER A 4 12.382 7.677 0.000 1.00 0.00 N
47
+ ATOM 46 H SER A 4 11.906 8.568 0.000 1.00 0.00 H
48
+ ATOM 47 CA SER A 4 13.831 7.677 0.000 1.00 0.00 C
49
+ ATOM 48 HA SER A 4 14.195 7.163 0.890 1.00 0.00 H
50
+ ATOM 49 CB SER A 4 14.380 6.966 -1.232 1.00 0.00 C
51
+ ATOM 50 HB2 SER A 4 14.032 5.933 -1.241 1.00 0.00 H
52
+ ATOM 51 HB3 SER A 4 14.032 7.474 -2.131 1.00 0.00 H
53
+ ATOM 52 OG SER A 4 15.809 6.986 -1.197 1.00 0.00 O
54
+ ATOM 53 HG SER A 4 16.155 6.538 -1.973 1.00 0.00 H
55
+ ATOM 54 C SER A 4 14.379 9.097 0.000 1.00 0.00 C
56
+ ATOM 55 O SER A 4 13.616 10.060 0.000 1.00 0.00 O
57
+ ATOM 56 OXT SER A 4 15.666 9.047 0.050 1.00 0.00 O
58
+ TER 57 SER A 4
59
+ END
4AA-huge/test/CMTS-traj-time.npy ADDED
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4AA-huge/test/CSFQ-traj-arrays.npz ADDED
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1
+ version https://git-lfs.github.com/spec/v1
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4AA-huge/test/CSFQ-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-18
2
+ ATOM 1 N CYS A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 CYS A 1 2.494 1.321 0.840 1.00 0.00 H
4
+ ATOM 3 H3 CYS A 1 2.643 1.440 -0.987 1.00 0.00 H
5
+ ATOM 4 H CYS A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA CYS A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA CYS A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB CYS A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB2 CYS A 1 2.497 3.801 1.241 1.00 0.00 H
10
+ ATOM 9 HB3 CYS A 1 3.877 3.116 2.131 1.00 0.00 H
11
+ ATOM 10 SG CYS A 1 4.310 5.304 1.366 1.00 0.00 S
12
+ ATOM 11 HG CYS A 1 3.725 5.622 2.518 1.00 0.00 H
13
+ ATOM 12 C CYS A 1 5.486 2.705 0.000 1.00 0.00 C
14
+ ATOM 13 O CYS A 1 6.009 1.593 0.000 1.00 0.00 O
15
+ ATOM 14 N SER A 2 6.191 3.839 0.000 1.00 0.00 N
16
+ ATOM 15 H SER A 2 5.715 4.730 0.000 1.00 0.00 H
17
+ ATOM 16 CA SER A 2 7.640 3.839 0.000 1.00 0.00 C
18
+ ATOM 17 HA SER A 2 8.004 3.325 0.890 1.00 0.00 H
19
+ ATOM 18 CB SER A 2 8.189 3.127 -1.232 1.00 0.00 C
20
+ ATOM 19 HB2 SER A 2 7.841 2.094 -1.241 1.00 0.00 H
21
+ ATOM 20 HB3 SER A 2 7.841 3.636 -2.131 1.00 0.00 H
22
+ ATOM 21 OG SER A 2 9.618 3.148 -1.197 1.00 0.00 O
23
+ ATOM 22 HG SER A 2 9.964 2.700 -1.973 1.00 0.00 H
24
+ ATOM 23 C SER A 2 8.188 5.259 0.000 1.00 0.00 C
25
+ ATOM 24 O SER A 2 7.425 6.222 0.000 1.00 0.00 O
26
+ ATOM 25 N PHE A 3 9.517 5.386 0.000 1.00 0.00 N
27
+ ATOM 26 H PHE A 3 10.103 4.564 0.000 1.00 0.00 H
28
+ ATOM 27 CA PHE A 3 10.161 6.684 0.000 1.00 0.00 C
29
+ ATOM 28 HA PHE A 3 9.863 7.239 -0.890 1.00 0.00 H
30
+ ATOM 29 CB PHE A 3 9.768 7.492 1.232 1.00 0.00 C
31
+ ATOM 30 HB2 PHE A 3 8.688 7.640 1.241 1.00 0.00 H
32
+ ATOM 31 HB3 PHE A 3 10.068 6.954 2.131 1.00 0.00 H
33
+ ATOM 32 CG PHE A 3 10.392 8.865 1.321 1.00 0.00 C
34
+ ATOM 33 CD1 PHE A 3 10.103 9.696 2.410 1.00 0.00 C
35
+ ATOM 34 HD1 PHE A 3 9.427 9.352 3.193 1.00 0.00 H
36
+ ATOM 35 CE1 PHE A 3 10.681 10.968 2.492 1.00 0.00 C
37
+ ATOM 36 HE1 PHE A 3 10.456 11.615 3.340 1.00 0.00 H
38
+ ATOM 37 CZ PHE A 3 11.549 11.409 1.486 1.00 0.00 C
39
+ ATOM 38 HZ PHE A 3 11.999 12.400 1.550 1.00 0.00 H
40
+ ATOM 39 CE2 PHE A 3 11.838 10.578 0.397 1.00 0.00 C
41
+ ATOM 40 HE2 PHE A 3 12.513 10.921 -0.386 1.00 0.00 H
42
+ ATOM 41 CD2 PHE A 3 11.259 9.306 0.315 1.00 0.00 C
43
+ ATOM 42 HD2 PHE A 3 11.485 8.659 -0.533 1.00 0.00 H
44
+ ATOM 43 C PHE A 3 11.677 6.544 0.000 1.00 0.00 C
45
+ ATOM 44 O PHE A 3 12.200 5.432 0.000 1.00 0.00 O
46
+ ATOM 45 N GLN A 4 12.382 7.677 0.000 1.00 0.00 N
47
+ ATOM 46 H GLN A 4 11.906 8.568 0.000 1.00 0.00 H
48
+ ATOM 47 CA GLN A 4 13.831 7.677 0.000 1.00 0.00 C
49
+ ATOM 48 HA GLN A 4 14.195 7.163 0.890 1.00 0.00 H
50
+ ATOM 49 CB GLN A 4 14.380 6.966 -1.232 1.00 0.00 C
51
+ ATOM 50 HB2 GLN A 4 14.032 5.933 -1.241 1.00 0.00 H
52
+ ATOM 51 HB3 GLN A 4 14.032 7.474 -2.131 1.00 0.00 H
53
+ ATOM 52 CG GLN A 4 15.904 6.987 -1.195 1.00 0.00 C
54
+ ATOM 53 HG2 GLN A 4 16.253 8.020 -1.186 1.00 0.00 H
55
+ ATOM 54 HG3 GLN A 4 16.253 6.479 -0.296 1.00 0.00 H
56
+ ATOM 55 CD GLN A 4 16.492 6.286 -2.410 1.00 0.00 C
57
+ ATOM 56 OE1 GLN A 4 15.757 5.793 -3.263 1.00 0.00 O
58
+ ATOM 57 NE2 GLN A 4 17.824 6.241 -2.488 1.00 0.00 N
59
+ ATOM 58 HE21 GLN A 4 18.266 5.786 -3.275 1.00 0.00 H
60
+ ATOM 59 HE22 GLN A 4 18.384 6.661 -1.760 1.00 0.00 H
61
+ ATOM 60 C GLN A 4 14.379 9.097 0.000 1.00 0.00 C
62
+ ATOM 61 O GLN A 4 13.616 10.060 0.000 1.00 0.00 O
63
+ ATOM 62 OXT GLN A 4 15.667 9.054 0.027 1.00 0.00 O
64
+ TER 63 GLN A 4
65
+ END
4AA-huge/test/CSFQ-traj-time.npy ADDED
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+ oid sha256:9a8a521cfb2ad58ef1d56a68b8111c31fd68b6ea71f8e01c4177604364390e39
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4AA-huge/test/CSGS-traj-arrays.npz ADDED
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1
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4AA-huge/test/CSGS-traj-state0.pdb ADDED
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1
+ REMARK 1 CREATED WITH OPENMM 7.7, 2023-01-21
2
+ ATOM 1 N CYS A 1 3.326 1.548 0.000 1.00 0.00 N
3
+ ATOM 2 H2 CYS A 1 2.658 1.443 -0.998 1.00 0.00 H
4
+ ATOM 3 H3 CYS A 1 2.481 1.313 0.824 1.00 0.00 H
5
+ ATOM 4 H CYS A 1 3.909 0.724 0.000 1.00 0.00 H
6
+ ATOM 5 CA CYS A 1 3.970 2.846 0.000 1.00 0.00 C
7
+ ATOM 6 HA CYS A 1 3.672 3.400 -0.890 1.00 0.00 H
8
+ ATOM 7 CB CYS A 1 3.577 3.654 1.232 1.00 0.00 C
9
+ ATOM 8 HB2 CYS A 1 2.497 3.801 1.241 1.00 0.00 H
10
+ ATOM 9 HB3 CYS A 1 3.877 3.116 2.131 1.00 0.00 H
11
+ ATOM 10 SG CYS A 1 4.310 5.304 1.366 1.00 0.00 S
12
+ ATOM 11 HG CYS A 1 3.725 5.622 2.518 1.00 0.00 H
13
+ ATOM 12 C CYS A 1 5.486 2.705 0.000 1.00 0.00 C
14
+ ATOM 13 O CYS A 1 6.009 1.593 0.000 1.00 0.00 O
15
+ ATOM 14 N SER A 2 6.191 3.839 0.000 1.00 0.00 N
16
+ ATOM 15 H SER A 2 5.715 4.730 0.000 1.00 0.00 H
17
+ ATOM 16 CA SER A 2 7.640 3.839 0.000 1.00 0.00 C
18
+ ATOM 17 HA SER A 2 8.004 3.325 0.890 1.00 0.00 H
19
+ ATOM 18 CB SER A 2 8.189 3.127 -1.232 1.00 0.00 C
20
+ ATOM 19 HB2 SER A 2 7.841 2.094 -1.241 1.00 0.00 H
21
+ ATOM 20 HB3 SER A 2 7.841 3.636 -2.131 1.00 0.00 H
22
+ ATOM 21 OG SER A 2 9.618 3.148 -1.197 1.00 0.00 O
23
+ ATOM 22 HG SER A 2 9.964 2.700 -1.973 1.00 0.00 H
24
+ ATOM 23 C SER A 2 8.188 5.259 0.000 1.00 0.00 C
25
+ ATOM 24 O SER A 2 7.425 6.222 0.000 1.00 0.00 O
26
+ ATOM 25 N GLY A 3 9.517 5.386 0.000 1.00 0.00 N
27
+ ATOM 26 H GLY A 3 10.103 4.564 0.000 1.00 0.00 H
28
+ ATOM 27 CA GLY A 3 10.161 6.684 0.000 1.00 0.00 C
29
+ ATOM 28 HA2 GLY A 3 9.863 7.239 -0.890 1.00 0.00 H
30
+ ATOM 29 HA3 GLY A 3 9.863 7.239 0.890 1.00 0.00 H
31
+ ATOM 30 C GLY A 3 11.675 6.525 0.000 1.00 0.00 C
32
+ ATOM 31 O GLY A 3 12.184 5.407 0.000 1.00 0.00 O
33
+ ATOM 32 N SER A 4 12.394 7.650 0.000 1.00 0.00 N
34
+ ATOM 33 H SER A 4 11.929 8.547 0.000 1.00 0.00 H
35
+ ATOM 34 CA SER A 4 13.843 7.632 0.000 1.00 0.00 C
36
+ ATOM 35 HA SER A 4 14.200 7.114 0.890 1.00 0.00 H
37
+ ATOM 36 CB SER A 4 14.383 6.914 -1.232 1.00 0.00 C
38
+ ATOM 37 HB2 SER A 4 14.022 5.886 -1.241 1.00 0.00 H
39
+ ATOM 38 HB3 SER A 4 14.041 7.427 -2.131 1.00 0.00 H
40
+ ATOM 39 OG SER A 4 15.813 6.917 -1.197 1.00 0.00 O
41
+ ATOM 40 HG SER A 4 16.153 6.465 -1.973 1.00 0.00 H
42
+ ATOM 41 C SER A 4 14.408 9.045 0.000 1.00 0.00 C
43
+ ATOM 42 O SER A 4 13.657 10.018 0.000 1.00 0.00 O
44
+ ATOM 43 OXT SER A 4 15.694 8.977 0.052 1.00 0.00 O
45
+ TER 44 SER A 4
46
+ END
4AA-huge/test/CSGS-traj-time.npy ADDED
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1
+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:32be7b0c5c511e0c01b3ce50766496cdde83aa3ecf50b56750ba9ee7a79a4186
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