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comparison test-data/check_compare_energy.txt @ 15:4f371a6a30d4 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
author chemteam
date Tue, 12 Jul 2022 12:47:30 +0000
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14:25b8272872c8 15:4f371a6a30d4
1 :-) GROMACS - gmx check, 2022-conda_forge (-:
2
3 Executable: /usr/local/bin.AVX2_256/gmx
4 Data prefix: /usr/local
5 Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working
6 Command line:
7 gmx check -e ./ener1.edr -e2 ./ener2.edr -tol 0.1 -abstol 0.1 -lastener Pressure
8
9 Opened ./ener1.edr as single precision energy file
10 Opened ./ener2.edr as single precision energy file
11
12 Reading energy frame 0 time 0.000
13 Reading energy frame 0 time 0.000
14 Reading energy frame 1 time 1.000
15 Reading energy frame 1 time 0.100
16 Reading energy frame 2 time 2.000
17 Reading energy frame 2 time 0.200
18 Reading energy frame 3 time 3.000
19 Reading energy frame 3 time 0.300
20 Reading energy frame 4 time 4.000
21 Reading energy frame 4 time 0.400 comparing energy file ./ener1.edr and ./ener2.edr
22
23 There are 31 and 50 terms in the energy files
24
25 enm[0] (Bond - -)
26 enm[30] (T-rest - -)
27 enm[6] (- - Disper. corr.)
28 enm[10] (- - Kinetic En.)
29 enm[11] (- - Total Energy)
30 enm[12] (- - Conserved En.)
31 enm[13] (- - Temperature)
32 enm[14] (- - Pres. DC)
33 enm[16] (- - Constr. rmsd)
34 enm[17] (- - Box-X)
35 enm[18] (- - Box-Y)
36 enm[19] (- - Box-Z)
37 enm[20] (- - Volume)
38 enm[21] (- - Density)
39 enm[22] (- - pV)
40 enm[23] (- - Enthalpy)
41 enm[43] (- - Box-Vel-XX)
42 enm[44] (- - Box-Vel-YY)
43 enm[45] (- - Box-Vel-ZZ)
44 enm[46] (- - T-Protein)
45 enm[47] (- - T-non-Protein)
46 enm[48] (- - Lamb-Protein)
47 enm[49] (- - Lamb-non-Protein)
48 There are 11 terms to compare in the energy files
49
50 Angle step 0: 659.741, step 0: 174.95
51 Proper Dih. step 0: 93.8665, step 0: 8.40722
52 Ryckaert-Bell. step 0: 69.404, step 0: 91.4765
53 Coulomb-14 step 0: 52.8221, step 0: 135.375
54 LJ (SR) step 0: -13.3421, step 0: -8.41078
55 Coulomb (SR) step 0: -1790.86, step 0: -2038.4
56 Coul. recip. step 0: 959.265, step 0: 615.944
57 Potential step 0: 618.021, step 0: -875.856
58 Pressure step 0: 901.187, step 0: 149.004
59 Vir-XX step 0: -2075.14, step 0: -98.9118
60 t (1.000000e+00 - 1.000000e-01)
61 step (1 - 50)
62 Angle step 1: 536.268, step 1: 188.647
63 Proper Dih. step 1: 88.2, step 1: 17.982
64 Ryckaert-Bell. step 1: 67.8373, step 1: 95.8567
65 Coulomb-14 step 1: 49.6531, step 1: 108.883
66 LJ (SR) step 1: -11.6246, step 1: 9.77759
67 Coulomb (SR) step 1: -1784.23, step 1: -2034.55
68 Coul. recip. step 1: 951.94, step 1: 546.933
69 Potential step 1: 230.009, step 1: -937.817
70 Pressure step 1: 893.094, step 1: 60.2446
71 Vir-XX step 1: -1778.72, step 1: 128.956
72 t (2.000000e+00 - 2.000000e-01)
73 step (2 - 100)
74 Angle step 2: 424.105, step 2: 176.128
75 Proper Dih. step 2: 81.0497, step 2: 13.4277
76 Ryckaert-Bell. step 2: 66.1758, step 2: 112.768
77 Coulomb-14 step 2: 47.7305, step 2: 126.537
78 LJ (SR) step 2: -0.367874, step 2: -9.48936
79 Coulomb (SR) step 2: -1780.95, step 2: -2085.56
80 Coul. recip. step 2: 946.125, step 2: 455.54
81 Potential step 2: -14.5562, step 2: -1076.08
82 Pressure step 2: 675.983, step 2: -57.99
83 Vir-XX step 2: -1371.69, step 2: 247.454
84 t (3.000000e+00 - 3.000000e-01)
85 step (3 - 150)
86 Angle step 3: 237.376, step 3: 205.981
87 Proper Dih. step 3: 68.1909, step 3: 18.2245
88 Ryckaert-Bell. step 3: 59.979, step 3: 147.317
89 Coulomb-14 step 3: 46.4965, step 3: 109.053
90 LJ (SR) step 3: -1.62034, step 3: 38.8948
91 Coulomb (SR) step 3: -1772, step 3: -2168.63
92 Coul. recip. step 3: 935.019, step 3: 399.011
93 Potential step 3: -223.77, step 3: -1128.1
94 Pressure step 3: 525.266, step 3: 37.3865
95 Vir-XX step 3: -964.61, step 3: 59.3395
96 t (4.000000e+00 - 4.000000e-01)
97 step (4 - 200)
98 Proper Dih. step 4: 59.4324, step 4: 17.8104
99 Ryckaert-Bell. step 4: 58.0578, step 4: 110.021
100 Coulomb-14 step 4: 48.4256, step 4: 105.922
101 LJ (SR) step 4: -5.24827, step 4: 17.1558
102 Coulomb (SR) step 4: -1769.41, step 4: -2150.06
103 Coul. recip. step 4: 932.888, step 4: 375.412
104 Potential step 4: -294.892, step 4: -1194.59
105 Pressure step 4: 242.456, step 4: 62.96
106 Vir-XX step 4: -736.257,
107 Reading energy frame 5 time 5.000
108 Reading energy frame 5 time 0.500
109 Reading energy frame 6 time 7.000
110 Reading energy frame 6 time 0.600
111 Reading energy frame 7 time 8.000
112 Reading energy frame 7 time 0.700
113 Reading energy frame 8 time 10.000
114 Reading energy frame 8 time 0.800
115 Reading energy frame 9 time 12.000
116 Reading energy frame 9 time 0.900
117 Reading energy frame 10 time 14.000
118 Reading energy frame 10 time 1.000 step 4: -3.54811
119 t (5.000000e+00 - 5.000000e-01)
120 step (5 - 250)
121 Angle step 5: 92.7917, step 5: 228.041
122 Proper Dih. step 5: 46.4461, step 5: 11.5992
123 Ryckaert-Bell. step 5: 53.249, step 5: 93.8753
124 Coulomb-14 step 5: 48.2479, step 5: 114.191
125 LJ (SR) step 5: -18.7401, step 5: 69.11
126 Coulomb (SR) step 5: -1763.71, step 5: -2209.02
127 Coul. recip. step 5: 923.209, step 5: 341.94
128 Potential step 5: -341.667, step 5: -1229.05
129 Pressure step 5: 356.299, step 5: 17.7417
130 Vir-XX step 5: -534.09, step 5: -113.967
131 t (7.000000e+00 - 6.000000e-01)
132 step (7 - 300)
133 Angle step 7: 130.86, step 7: 193.185
134 Proper Dih. step 7: 42.6816, step 7: 7.0615
135 Ryckaert-Bell. step 7: 53.3748, step 7: 106.945
136 Coulomb-14 step 7: 49.9217, step 7: 100.896
137 LJ (SR) step 7: -15.5538, step 7: 10.2121
138 Coulomb (SR) step 7: -1764.3, step 7: -2143.78
139 Coul. recip. step 7: 924.347, step 7: 311.339
140 Potential step 7: -444.809, step 7: -1304.87
141 Pressure step 7: 215.786, step 7: -61.3894
142 Vir-XX step 7: -589.888, step 7: 192.034
143 t (8.000000e+00 - 7.000000e-01)
144 step (8 - 350)
145 Angle step 8: 68.783, step 8: 187.181
146 Proper Dih. step 8: 30.5271, step 8: 10.9997
147 Ryckaert-Bell. step 8: 49.841, step 8: 123.72
148 Coulomb-14 step 8: 51.1761, step 8: 123.582
149 LJ (SR) step 8: -24.7767, step 8: 48.0457
150 Coulomb (SR) step 8: -1761.91, step 8: -2227.32
151 Coul. recip. step 8: 918.219, step 8: 267.376
152 Potential step 8: -447.838, step 8: -1356
153 Pressure step 8: 255.303, step 8: -36.2835
154 Vir-XX step 8: -410.784, step 8: 5.87002
155 t (1.000000e+01 - 8.000000e-01)
156 step (10 - 400)
157 Angle step 10: 90.876, step 10: 150.124
158 Proper Dih. step 10: 26.773, step 10: 15.4228
159 Ryckaert-Bell. step 10: 49.7648, step 10: 116.734
160 Coulomb-14 step 10: 52.0739, step 10: 120.921
161 LJ (SR) step 10: -24.2058, step 10: 61.3815
162 Coulomb (SR) step 10: -1762.32, step 10: -2208.19
163 Coul. recip. step 10: 918.133, step 10: 281.327
164 Potential step 10: -522.879, step 10: -1339
165 Pressure step 10: 177.827, step 10: 95.8529
166 Vir-XX step 10: -466.151, step 10: 18.0131
167 t (1.200000e+01 - 9.000000e-01)
168 step (12 - 450)
169 Angle step 12: 71.9619, step 12: 218.415
170 Proper Dih. step 12: 20.7858, step 12: 6.46661
171 Ryckaert-Bell. step 12: 48.0374, step 12: 118.772
172 LJ-14 step 12: 113.003, step 12: 125.421
173 Coulomb-14 step 12: 53.485, step 12: 111.128
174 LJ (SR) step 12: -27.637, step 12: 39.4093
175 Coulomb (SR) step 12: -1762.36, step 12: -2201.92
176 Coul. recip. step 12: 915.934, step 12: 272.022
177 Potential step 12: -542.18, step 12: -1310.71
178 Pressure step 12: 180.996, step 12: -77.3705
179 Vir-XX step 12: -403.068, step 12: -3.89205
180 t (1.400000e+01 - 1.000000e+00)
181 step (14 - 500)
182 Angle step 14: 77.708, step 14: 188.913
183 Proper Dih. step 14: 16.917, step 14: 13.1638
184 Ryckaert-Bell. step 14: 47.5084, step 14: 116.045
185 LJ-14 step 14: 112.831, step 14: 128.155
186 Coulomb-14 step 14: 54.3835, step 14: 112.113
187 LJ (SR) step 14: -29.3721, step 14: 18.6406
188 Coulomb (SR) step 1
189 Reading energy frame 11 time 15.000
190 Last energy frame read 10 time 1.000
191 GROMACS reminds you: "I do not believe continuum electrostatics" (Arieh Warshel, Nobel lecture 2013)
192
193 4: -1762.94, step 14: -2187.48
194 Coul. recip. step 14: 914.559, step 14: 304.201
195 Potential step 14: -557.441, step 14: -1306.67
196 Pressure step 14: 144.996, step 14: -10.3104
197 Vir-XX step 14: -396.739, step 14: 362.156
198
199 End of file on ./ener2.edr but not on ./ener1.edr