1 // ******************************************************************************
2 //
3 // Title: Force Field X.
4 // Description: Force Field X - Software for Molecular Biophysics.
5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2024.
6 //
7 // This file is part of Force Field X.
8 //
9 // Force Field X is free software; you can redistribute it and/or modify it
10 // under the terms of the GNU General Public License version 3 as published by
11 // the Free Software Foundation.
12 //
13 // Force Field X is distributed in the hope that it will be useful, but WITHOUT
14 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
15 // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
16 // details.
17 //
18 // You should have received a copy of the GNU General Public License along with
19 // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
20 // Place, Suite 330, Boston, MA 02111-1307 USA
21 //
22 // Linking this library statically or dynamically with other modules is making a
23 // combined work based on this library. Thus, the terms and conditions of the
24 // GNU General Public License cover the whole combination.
25 //
26 // As a special exception, the copyright holders of this library give you
27 // permission to link this library with independent modules to produce an
28 // executable, regardless of the license terms of these independent modules, and
29 // to copy and distribute the resulting executable under terms of your choice,
30 // provided that you also meet, for each linked independent module, the terms
31 // and conditions of the license of that module. An independent module is a
32 // module which is not derived from or based on this library. If you modify this
33 // library, you may extend this exception to your version of the library, but
34 // you are not obligated to do so. If you do not wish to do so, delete this
35 // exception statement from your version.
36 //
37 // ******************************************************************************
38 package ffx.potential.groovy;
39
40 import org.junit.runner.RunWith;
41 import org.junit.runners.Parameterized;
42 import org.junit.runners.Parameterized.Parameters;
43
44 import java.util.Arrays;
45 import java.util.Collection;
46
47 /**
48 * Test the Energy script.
49 */
50 @RunWith(Parameterized.class)
51 public class EnergyTest extends ParentEnergyTest {
52
53 public EnergyTest(String info, String filename, int nAtoms, double bondEnergy, int nBonds,
54 double angleEnergy, int nAngles, double stretchBendEnergy, int nStretchBends,
55 double ureyBradleyEnergy, int nUreyBradleys, double outOfPlaneBendEnergy,
56 int nOutOfPlaneBends, double torsionEnergy, int nTorsions, double improperTorsionEnergy,
57 int nImproperTorsions, double piOrbitalTorsionEnergy, int nPiOrbitalTorsions,
58 double torsionTorsionEnergy, int nTorsionTorsions, double stretchTorsionEnergy,
59 int nStretchTorsions, double angleTorsionEnergy, int nAngleTorsions, double vanDerWaalsEnergy,
60 int nVanDerWaals, double permanentEnergy, int nPermanent, double polarizationEnergy,
61 int nPolar, double gkEnergy, int nGK, boolean testOpenMM) {
62 super(info, filename, nAtoms, bondEnergy, nBonds, angleEnergy, nAngles, stretchBendEnergy, nStretchBends,
63 ureyBradleyEnergy, nUreyBradleys, outOfPlaneBendEnergy, nOutOfPlaneBends, torsionEnergy,
64 nTorsions, improperTorsionEnergy, nImproperTorsions, piOrbitalTorsionEnergy,
65 nPiOrbitalTorsions, torsionTorsionEnergy, nTorsionTorsions, stretchTorsionEnergy,
66 nStretchTorsions, angleTorsionEnergy, nAngleTorsions, vanDerWaalsEnergy, nVanDerWaals,
67 permanentEnergy, nPermanent, polarizationEnergy, nPolar, gkEnergy, nGK, testOpenMM);
68 }
69
70 @Parameters
71 public static Collection<Object[]> data() {
72 return Arrays.asList(
73 new Object[][]{
74 {
75 "SNARE P212121",
76 "1n7s.P212121.xyz",
77 5357,
78 351.32142483,
79 5040,
80 744.19251364,
81 8255,
82 6.42015744,
83 6924,
84 2.50163831,
85 322,
86 135.24919366,
87 2487,
88 417.89244418,
89 11449,
90 0.0,
91 0,
92 39.85643934,
93 370,
94 -560.99576469,
95 268,
96 0.0,
97 0,
98 0.0,
99 0,
100 4003.27183547,
101 741643,
102 -12303.93157019,
103 332114,
104 -2811.45683671,
105 332114,
106 0.0,
107 0,
108 false
109 },
110 {
111 // OpenMM does not handle this correctly yet.
112 "SNARE P1",
113 "1n7s.P1.xyz",
114 21428,
115 1405.28569930,
116 20160,
117 2976.77005458,
118 33020,
119 25.68062976,
120 27696,
121 10.00655326,
122 1288,
123 540.99677465,
124 9948,
125 1671.56977674,
126 45796,
127 0.0,
128 0,
129 159.42575736,
130 1480,
131 -2243.98305878,
132 1072,
133 0.0,
134 0,
135 0.0,
136 0,
137 16013.08734188,
138 2966572,
139 -49215.72628076,
140 1328456,
141 -11245.82734685,
142 1328456,
143 0.0,
144 0,
145 false
146 },
147 {
148 "DHFR Benchmark",
149 "dhfr.xyz",
150 23558,
151 6623.70878543,
152 16569,
153 4748.78155255,
154 11584,
155 -19.78973386,
156 4031,
157 -132.74781407,
158 7023,
159 110.84355342,
160 1566,
161 433.69593807,
162 6701,
163 0.0,
164 0,
165 58.75073806,
166 292,
167 -41.99981847,
168 147,
169 0.0,
170 0,
171 0.0,
172 0,
173 31718.84803063,
174 3480619,
175 -78751.36662993,
176 1463589,
177 -31790.15161303,
178 1463589,
179 0.0,
180 0,
181 true
182 },
183 {
184 "AMBER99SB GB (no dispersion) Capped DMHD",
185 "dmhd-amber99sb.xyz",
186 71,
187 1.56331971,
188 71,
189 25.07578077,
190 124,
191 0.0,
192 0,
193 0.0,
194 0,
195 0.0,
196 0,
197 27.92653816,
198 169,
199 0.15162117,
200 20,
201 0.0,
202 0,
203 0.0,
204 0,
205 0.0,
206 0,
207 0.0,
208 0,
209 -4.31922323,
210 2290,
211 -71.00737570,
212 2290,
213 0.0,
214 2290,
215 -184.01591119210968,
216 2556,
217 true
218 },
219 {
220 "AMOEBA Bio 2018 Crambin GK/SA",
221 "crambin.xyz",
222 642,
223 134.83946761,
224 652,
225 133.94053912,
226 1183,
227 -4.81704334,
228 1044,
229 0.0,
230 0,
231 29.92634330,
232 375,
233 18.82386314,
234 1747,
235 0.0,
236 0,
237 12.01761948,
238 66,
239 -23.33097186,
240 4,
241 0.0,
242 0,
243 0.0,
244 0,
245 308.55702420206063,
246 203926,
247 -1208.3841483371093, // -1208.54202510
248 203926,
249 -127.5927132059615, // -127.41736039
250 203926,
251 -203.68131916301343, // -203.76192317960601
252 206403,
253 false
254 },
255 {
256 "AMOEBA Protein 2013 GK Capped DMHD",
257 "dmhd-amoebapro13.xyz",
258 71,
259 4.00030221,
260 71,
261 15.27574588,
262 124,
263 -0.23989418,
264 110,
265 0.0,
266 0,
267 0.39337245,
268 51,
269 3.40745668,
270 169,
271 0.0,
272 0,
273 0.09663007,
274 10,
275 0.0,
276 0,
277 0.0,
278 0,
279 0.0,
280 0,
281 20.36671513,
282 2290,
283 -169.05487037936405, // -169.03958434,
284 2290,
285 -25.8482461594885, // -25.85878386
286 2290,
287 -207.4485546982137, // -207.47535790184864
288 2556,
289 true
290 },
291 {
292 "AMOEBA 2009 Tetra-Alanine GK",
293 "alatet.int",
294 42,
295 1.66598227,
296 41,
297 3.41765862,
298 72,
299 -0.07860298,
300 57,
301 0.0,
302 0,
303 0.29369677,
304 24,
305 7.99325266,
306 91,
307 0.0,
308 0,
309 0.01292169,
310 4,
311 1.95288364,
312 3,
313 0.0,
314 0,
315 0.0,
316 0,
317 20.39805900,
318 748,
319 -78.53945229,
320 748,
321 -8.62910979,
322 748,
323 -59.70833911386979,
324 903,
325 false
326 },
327 {
328 "Amber99sb Peptide",
329 "peptide-amber99sb.xyz",
330 328,
331 41.19699756,
332 333,
333 54.88751601,
334 596,
335 0.0,
336 0,
337 0.0,
338 0,
339 0.0,
340 0,
341 189.34195768,
342 875,
343 1.59062194,
344 101,
345 0.0,
346 0,
347 0.0,
348 0,
349 0.0,
350 0,
351 0.0,
352 0,
353 111362.79687915,
354 52696,
355 -413.52897447,
356 52699,
357 0.0,
358 52699,
359 0.0,
360 0,
361 true
362 },
363 {
364 "Ubiquitin Benchmark",
365 "ubiquitin.xyz",
366 9737,
367 2856.59378034,
368 6908,
369 2018.16571190,
370 5094,
371 -6.98794687,
372 1958,
373 -55.63461732,
374 2835,
375 65.00809012,
376 651,
377 224.37608631,
378 3297,
379 0.0,
380 0,
381 20.43063520,
382 106,
383 -31.48011891,
384 71,
385 0.0,
386 0,
387 0.0,
388 0,
389 12862.34983956,
390 1482946,
391 -32737.08497141565, // or -32736.92207773 (with no FFT factors of 6 & 7)
392 623627,
393 -12934.94219259, // or -12934.93512829 (with no FFT factors of 6 & 7)
394 623627,
395 0.0,
396 0,
397 true
398 },
399 {
400 "Ubiquitin Amber 1999 Benchmark",
401 "ubiquitin-amber99.xyz",
402 9737,
403 3496.26834781,
404 6908,
405 2056.15089674,
406 5094,
407 0.0,
408 0,
409 0.0,
410 0,
411 0.0,
412 0,
413 705.79420086,
414 3297,
415 27.59366005,
416 287,
417 0.0,
418 0,
419 0.0,
420 0,
421 0.0,
422 0,
423 0.0,
424 0,
425 4860.41072437,
426 2279196,
427 -40036.04804903,
428 3562034,
429 0.0,
430 3562034,
431 0.0,
432 0,
433 true
434 },
435 {
436 "Acetanilide Benchmark",
437 "acetanilide.xyz",
438 19,
439 0.67814832,
440 19,
441 1.06817134,
442 30,
443 -0.06290501,
444 26,
445 0.0,
446 0,
447 0.13033970,
448 24,
449 -8.01262794,
450 38,
451 0.0,
452 0,
453 0.0,
454 0,
455 0.0,
456 0,
457 0.0,
458 0,
459 0.0,
460 0,
461 -3.62572228,
462 7295,
463 -26.0720131242538,
464 2231,
465 -1.9856761645305,
466 2231,
467 0.0,
468 0,
469 false
470 },
471 {
472 "Ethylparaben Benchmark",
473 "ethylparaben.xyz",
474 44,
475 1.37991170,
476 44,
477 2.43600964,
478 70,
479 0.20006782,
480 58,
481 0.0,
482 0,
483 0.04434686,
484 42,
485 -7.14298308,
486 88,
487 0.0,
488 0,
489 0.0,
490 0,
491 0.0,
492 0,
493 0.0,
494 0,
495 0.0,
496 0,
497 -4.816366774263829,
498 32644,
499 -45.55012417320137,
500 5012,
501 -3.97079858673400,
502 5012,
503 0.0,
504 0,
505 false
506 },
507 {
508 "Methylparaben Benchmark",
509 "methylparaben.xyz",
510 19,
511 0.42501694,
512 19,
513 1.23611203,
514 29,
515 0.00351228,
516 24,
517 0.0,
518 0,
519 0.01058196,
520 21,
521 -3.72750990,
522 35,
523 0.0,
524 0,
525 0.0,
526 0,
527 0.0,
528 0,
529 0.0,
530 0,
531 0.0,
532 0,
533 0.20573979,
534 7639,
535 -26.558577471708134,
536 2314,
537 -2.35904592,
538 2314,
539 0.0,
540 0,
541 false
542 },
543 {
544 "Paracetamol Benchmark",
545 "paracetamol.xyz",
546 20,
547 0.55316710,
548 20,
549 1.51848706,
550 31,
551 0.05096337,
552 27,
553 0.0,
554 0,
555 0.46651316,
556 24,
557 -7.40125527,
558 40,
559 0.0,
560 0,
561 0.0,
562 0,
563 0.0,
564 0,
565 0.0,
566 0,
567 0.0,
568 0,
569 0.76621272,
570 7832,
571 -32.02011297249507,
572 2357,
573 -4.96649992387851,
574 2357,
575 0.0,
576 0,
577 false
578 },
579 {
580 "Phenacetin Benchmark",
581 "phenacetin.xyz",
582 26,
583 0.56492623,
584 26,
585 2.68273715,
586 43,
587 0.00409248,
588 35,
589 0.0,
590 0,
591 0.33385711,
592 24,
593 -6.49787814,
594 52,
595 0.0,
596 0,
597 0.0,
598 0,
599 0.0,
600 0,
601 0.0,
602 0,
603 0.0,
604 0,
605 -5.792072251098926,
606 20384,
607 -25.42173449818894,
608 3138,
609 -2.09385416786188,
610 3138,
611 0.0,
612 0,
613 false
614 }
615
616 });
617 }
618
619
620 }