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 with Generalized Kirkwood parameters.
49 */
50 @RunWith(Parameterized.class)
51 public class GKEnergyTest extends ParentEnergyTest {
52
53 public GKEnergyTest(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 * Test values for Solvation/GK/Atomic Multipoles/Polarization don't exactly match
76 * published values (Corrigan et. al. 2023) due to small multipole updates to the
77 * AMOEBA-BIO-2018 force field made in early 2023 to accommodate CpHMD work
78 *
79 * The error magnitude is <2 kcal for each term
80 */
81 {
82 "RNA (1mis) with GK from Corrigan et al (2023)",
83 "1mis.xyz",
84 522, // Atoms
85 60.88950457, // Bond
86 562,
87 136.35249695, // Angle
88 998,
89 2.43194433, // Stretch-Bend
90 848,
91 0.0, // Urey-Bradley
92 0,
93 0.10282386, // Out-of-Plane
94 294,
95 79.48824698, // Torsion
96 1492,
97 0.0, // Improper Torsion
98 0,
99 0.45934575, // Pi-Orbital Torsion
100 96,
101 0.0, // Torsion-Torsion
102 0,
103 -3.02691282, // Stretch-Torsion
104 44,
105 -4.54420615, // Angle-Torsion
106 72,
107 218.31775844, // vdW
108 134421,
109 875.03795766, // Permanent
110 134421,
111 -238.72680230, // Polarization
112 134421,
113 -3236.93867799, // Total Solvation
114 // Generalized Kirkwood -3221.37466819
115 // Cavitation 272.96015049, Dispersion -288.52416028
116 136503,
117 false
118 },
119 {
120 "RNA (1mis) with GK from Corrigan et al (2021)",
121 "1mis.gk2021.xyz",
122 522, // Atoms
123 60.88950457, // Bond
124 562,
125 136.35249695, // Angle
126 998,
127 2.43194433, // Stretch-Bend
128 848,
129 0.0, // Urey-Bradley
130 0,
131 0.10282386, // Out-of-Plane
132 294,
133 79.48824698, // Torsion
134 1492,
135 0.0, // Improper Torsion
136 0,
137 0.45934575, // Pi-Orbital Torsion
138 96,
139 0.0, // Torsion-Torsion
140 0,
141 -3.02691282, // Stretch-Torsion
142 44,
143 -4.54420615, // Angle-Torsion
144 72,
145 218.31775844, // vdW
146 134421,
147 875.03795766, // Permanent
148 134421,
149 -238.72700000, // Polarization
150 134421,
151 -3308.29464032, // Total Solvation
152 136503,
153 false
154 },
155 /*
156 * Test values for Solvation/GK/Atomic Multipoles/Polarization don't exactly match
157 * published values (Corrigan et. al. 2023) due to small multipole updates to the
158 * AMOEBA-BIO-2018 force field made in early 2023 to accommodate CpHMD work
159 *
160 * The error magnitude is <2 kcal for each term
161 */
162 {
163 "Protein (1bpi) with GK from Corrigan et al (2023)",
164 "1bpi.xyz",
165 892, // Atoms
166 281.75870048, // Bond
167 906,
168 235.11731039, // Angle
169 1626,
170 -12.11600646, // Stretch-Bend
171 1455,
172 0.0, // Urey-Bradley
173 0,
174 28.91012526, // Out-of-Plane
175 597,
176 69.15283653, // Torsion
177 2391,
178 0.0, // Improper Torsion
179 0,
180 27.49698981, // Pi-Orbital Torsion
181 109,
182 -36.43950083, // Torsion-Torsion
183 6,
184 0.0, // Stretch-Torsion
185 0,
186 0.0, // Angle-Torsion
187 0,
188 470.1728659015, // vdW
189 394854,
190 -1189.88505475, // Permanent
191 394854,
192 -242.15918841, // Polarization
193 394854,
194 -923.17087281, // Total Solvation
195 //Generalized Kirkwood -970.64995804
196 //Cavitation 444.79997963, Dispersion -397.32089439
197 398278,
198 false
199 },
200 /*
201 * Test values for Solvation/GK/Atomic Multipoles/Polarization don't exactly match
202 * published values (Corrigan et. al. 2023) due to small multipole updates to the
203 * AMOEBA-BIO-2018 force field made in early 2023 to accommodate CpHMD work
204 *
205 * The error magnitude is <2 kcal for each term
206 */
207 {
208 "Protein (1bpi) with GK from Corrigan et al (2023) - No Neck",
209 "1bpi.noneck.xyz",
210 892, // Atoms
211 281.75870048, // Bond
212 906,
213 235.11731039, // Angle
214 1626,
215 -12.11600646, // Stretch-Bend
216 1455,
217 0.0, // Urey-Bradley
218 0,
219 28.91012526, // Out-of-Plane
220 597,
221 69.15283653, // Torsion
222 2391,
223 0.0, // Improper Torsion
224 0,
225 27.49698981, // Pi-Orbital Torsion
226 109,
227 -36.43950083, // Torsion-Torsion
228 6,
229 0.0, // Stretch-Torsion
230 0,
231 0.0, // Angle-Torsion
232 0,
233 470.1728659015, // vdW
234 394854,
235 -1189.88505475, // Permanent
236 394854,
237 -242.15918841, // Polarization
238 394854,
239 -900.45662762, // Total Solvation
240 //Generalized Kirkwood -947.93571285
241 //Cavitation 444.79997963, Dispersion -397.32089439
242 398278,
243 false
244 },
245 /*
246 * Test values for Solvation/GK/Atomic Multipoles/Polarization don't exactly match
247 * published values (Corrigan et. al. 2023) due to small multipole updates to the
248 * AMOEBA-BIO-2018 force field made in early 2023 to accommodate CpHMD work
249 *
250 * The error magnitude is <2 kcal for each term
251 */
252 {
253 "Protein (1bpi) with GK from Corrigan et al (2023) - No Tanh",
254 "1bpi.notanh.xyz",
255 892, // Atoms
256 281.75870048, // Bond
257 906,
258 235.11731039, // Angle
259 1626,
260 -12.11600646, // Stretch-Bend
261 1455,
262 0.0, // Urey-Bradley
263 0,
264 28.91012526, // Out-of-Plane
265 597,
266 69.15283653, // Torsion
267 2391,
268 0.0, // Improper Torsion
269 0,
270 27.49698981, // Pi-Orbital Torsion
271 109,
272 -36.43950083, // Torsion-Torsion
273 6,
274 0.0, // Stretch-Torsion
275 0,
276 0.0, // Angle-Torsion
277 0,
278 470.1728659015, // vdW
279 394854,
280 -1189.88505475, // Permanent
281 394854,
282 -242.15918841, // Polarization
283 394854,
284 -1241.80712005, // Total Solvation
285 //Generalized Kirkwood -1289.28620528
286 //Cavitation 444.79997963, Dispersion -397.32089439
287 398278,
288 false
289 },
290 /*
291 * Test values for Solvation/GK/Atomic Multipoles/Polarization don't exactly match
292 * published values (Corrigan et. al. 2023) due to small multipole updates to the
293 * AMOEBA-BIO-2018 force field made in early 2023 to accommodate CpHMD work
294 *
295 * The error magnitude is <2 kcal for each term
296 */
297 {
298 "Protein (1bpi) with GK from Corrigan et al (2023) - No Neck, No Tanh",
299 "1bpi.noneck.notanh.xyz",
300 892, // Atoms
301 281.75870048, // Bond
302 906,
303 235.11731039, // Angle
304 1626,
305 -12.11600646, // Stretch-Bend
306 1455,
307 0.0, // Urey-Bradley
308 0,
309 28.91012526, // Out-of-Plane
310 597,
311 69.15283653, // Torsion
312 2391,
313 0.0, // Improper Torsion
314 0,
315 27.49698981, // Pi-Orbital Torsion
316 109,
317 -36.43950083, // Torsion-Torsion
318 6,
319 0.0, // Stretch-Torsion
320 0,
321 0.0, // Angle-Torsion
322 0,
323 470.1728659015, // vdW
324 394854,
325 -1189.88505475, // Permanent
326 394854,
327 -242.15918841, // Polarization
328 394854,
329 -1325.30614458, // Total Solvation
330 //Generalized Kirkwood -1372.78522981
331 //Cavitation 444.79997963, Dispersion -397.32089439
332 398278,
333 false
334 },
335 /*
336 * Test values for Solvation/GK/Atomic Multipoles/Polarization don't exactly match
337 * published values (Corrigan et. al. 2023) due to small multipole updates to the
338 * AMOEBA-BIO-2018 force field made in early 2023 to accommodate CpHMD work
339 *
340 * The error magnitude is <2 kcal for each term
341 */
342 {
343 "Protein (1bpi) with GK from Corrigan et al (2023) - No Element HCT or Interstitial Space Corrections",
344 "1bpi.noelemhct.xyz",
345 892, // Atoms
346 281.75870048, // Bond
347 906,
348 235.11731039, // Angle
349 1626,
350 -12.11600646, // Stretch-Bend
351 1455,
352 0.0, // Urey-Bradley
353 0,
354 28.91012526, // Out-of-Plane
355 597,
356 69.15283653, // Torsion
357 2391,
358 0.0, // Improper Torsion
359 0,
360 27.49698981, // Pi-Orbital Torsion
361 109,
362 -36.43950083, // Torsion-Torsion
363 6,
364 0.0, // Stretch-Torsion
365 0,
366 0.0, // Angle-Torsion
367 0,
368 470.1728659015, // vdW
369 394854,
370 -1189.88505475, // Permanent
371 394854,
372 -242.15918841, // Polarization
373 394854,
374 -1330.12099084, // Total Solvation
375 //Generalized Kirkwood -1377.60007607
376 //Cavitation 444.79997963, Dispersion -397.32089439
377 398278,
378 false
379 },
380 {
381 "Protein (1bpi) with GK from Corrigan et al (2021)",
382 "1bpi.gk2021.xyz",
383 892, // Atoms
384 281.75870048, // Bond
385 906,
386 235.11731039, // Angle
387 1626,
388 -12.11600646, // Stretch-Bend
389 1455,
390 0.0, // Urey-Bradley
391 0,
392 28.91012526, // Out-of-Plane
393 597,
394 69.15283653, // Torsion
395 2391,
396 0.0, // Improper Torsion
397 0,
398 27.49698981, // Pi-Orbital Torsion
399 109,
400 -36.43950083, // Torsion-Torsion
401 6,
402 0.0, // Stretch-Torsion
403 0,
404 0.0, // Angle-Torsion
405 0,
406 470.1728659015, // vdW
407 394854,
408 -1189.885054752826, // Permanent
409 394854,
410 -242.15918841434635, // Polarization
411 394854,
412 -1166.1124974225615, // Total Solvation
413 398278,
414 false
415 }
416
417 });
418 }
419
420
421 }