============================================== | | | C R E S T | | | | Conformer-Rotamer Ensemble Sampling Tool | | based on the GFNn-xTB methods | | P.Pracht, S.Grimme | | Universitaet Bonn, MCTC | ============================================== Version 2.10.2, Tue 9. Jun 13:32:10 CEST 2020 Using the xTB program. Compatible with XTB version 6.1 and later. Cite work conducted with this code as P. Pracht, F. Bohle, S. Grimme, PCCP, 2020, 22, 7169-7192. and S. Grimme, JCTC, 2019, 15, 2847-2862. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Command line input: > /usr/software/xtb/crest start.xyz -gfn2 -chrg 0 -uhf 1 -T 32 -gfn2 : Use of GFN2-xTB requested. -chrg 0 -uhf 1 -T 32 (CPUs/Threads selected) ".xcontrol" file present. content of the constraining file (sorted): > $wall > potential=logfermi > beta=10.0 > temp=6000.0 > ellipsoid: 20.0,12.0,12.0,all > $constrain > force constant=0.5 > distance: 1, 7, 2.05 > distance: 1, 4, 2.05 > distance: 1, 6, 2.05 > distance: 1, 5, 2.05 =========================================== WARNING: The input coordinate file would be sorted by zsort and a constraining file is present. To avoid constrainment of the wrong atoms zsort will be turned off. This also might influence the results. =========================================== ------------------------- xTB Geometry Optimization ------------------------- Geometry successfully optimized. ------------------------------------------------ Generating MTD length from a flexibility measure ------------------------------------------------ Calculating WBOs... done. flexibility measure : 0.065 t(MTD) / ps : 5.0 Σ(t(MTD)) / ps : 60.0 (+ 10.0) ------------------------------------- Starting a trial MTD to test settings ------------------------------------- Trial MTD 1 did not converge! Reducing the time step to 4 fs and trying again... Trial MTD 2 did not converge! Reducing the time step to 3 fs and trying again... Estimated runtime for one MTD (5.0 ps) on a single thread: 1 h 11 min 48 sec Estimated runtime for a batch of 14 MTDs on 32 threads: 35 min 54 sec list of Vbias parameters applied: $metadyn 0.00300 1.300 $metadyn 0.00150 1.300 $metadyn 0.00075 1.300 $metadyn 0.00300 0.780 $metadyn 0.00150 0.780 $metadyn 0.00075 0.780 $metadyn 0.00300 0.468 $metadyn 0.00150 0.468 $metadyn 0.00075 0.468 $metadyn 0.00300 0.281 $metadyn 0.00150 0.281 $metadyn 0.00075 0.281 $metadyn 0.00100 0.100 $metadyn 0.00500 0.800 ******************************************************************************************* ** N E W I T E R A T I O N C Y C L E ** ******************************************************************************************* ======================================== MTD Iteration 1 ======================================== ======================================== | Meta-MD (MTD) Sampling | ======================================== Starting Meta-MD 2 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0855 Vbias exponent(α) : 1.30 Starting Meta-MD 1 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.1710 Vbias exponent(α) : 1.30 Starting Meta-MD 3 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0428 Vbias exponent(α) : 1.30 Starting Meta-MD 4 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.1710 Vbias exponent(α) : 0.78 Starting Meta-MD 5 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0855 Vbias exponent(α) : 0.78 Starting Meta-MD 6 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0428 Vbias exponent(α) : 0.78 Starting Meta-MD 7 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.1710 Vbias exponent(α) : 0.47 Starting Meta-MD 8 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0855 Vbias exponent(α) : 0.47 Starting Meta-MD 9 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0428 Vbias exponent(α) : 0.47 Starting Meta-MD 10 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.1710 Vbias exponent(α) : 0.28 Starting Meta-MD 11 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0855 Vbias exponent(α) : 0.28 Starting Meta-MD 12 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0428 Vbias exponent(α) : 0.28 Starting Meta-MD 14 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.2850 Vbias exponent(α) : 0.80 Starting Meta-MD 13 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0570 Vbias exponent(α) : 0.10 *Meta-MD 4 finished* *Meta-MD 6 finished* *Meta-MD 12 finished* *Meta-MD 3 finished* *Meta-MD 5 finished* *Meta-MD 1 finished* *Meta-MD 10 finished* *Meta-MD 2 finished* *Meta-MD 8 finished* *Meta-MD 11 finished* *Meta-MD 9 finished* *Meta-MD 7 finished* *Meta-MD 13 finished* *Meta-MD 14 finished* ----------------------- Multilevel Optimization ----------------------- ------------------------- 1. crude pre-optimization ------------------------- writing TMPCONF* Dirs from file "crest_rotamers_0.xyz" ... done. Starting optimization of generated structures 700 jobs to do. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 done. Now appending opt.xyz file with new structures running RMSDs... done. E lowest : -94.77566 131 structures remain within 12.00 kcal/mol window ------------------------------------- 2. optimization with tight thresholds ------------------------------------- writing TMPCONF* Dirs from file "crest_rotamers_1.xyz" ... done. Starting optimization of generated structures 132 jobs to do. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 done. Now appending opt.xyz file with new structures running RMSDs... done. E lowest : -94.80589 12 structures remain within 6.00 kcal/mol window ======================================== MTD Iteration 2 ======================================== ======================================== | Meta-MD (MTD) Sampling | ======================================== Starting Meta-MD 1 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.1710 Vbias exponent(α) : 1.30 Starting Meta-MD 2 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0855 Vbias exponent(α) : 1.30 Starting Meta-MD 3 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0428 Vbias exponent(α) : 1.30 Starting Meta-MD 4 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.1710 Vbias exponent(α) : 0.78 Starting Meta-MD 5 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0855 Vbias exponent(α) : 0.78 Starting Meta-MD 6 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0428 Vbias exponent(α) : 0.78 Starting Meta-MD 7 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.1710 Vbias exponent(α) : 0.47 Starting Meta-MD 8 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0855 Vbias exponent(α) : 0.47 Starting Meta-MD 9 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0428 Vbias exponent(α) : 0.47 Starting Meta-MD 10 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.1710 Vbias exponent(α) : 0.28 Starting Meta-MD 11 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0855 Vbias exponent(α) : 0.28 Starting Meta-MD 12 with the settings: MD time /ps : 5.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 dumpstep(Vbias)/ps : 1.0 Vbias prefactor(k) : 0.0428 Vbias exponent(α) : 0.28 *Meta-MD 3 finished* *Meta-MD 1 finished* *Meta-MD 9 finished* *Meta-MD 10 finished* *Meta-MD 8 finished* *Meta-MD 11 finished* *Meta-MD 2 finished* *Meta-MD 5 finished* *Meta-MD 6 finished* *Meta-MD 4 finished* *Meta-MD 7 finished* *Meta-MD 12 finished* ----------------------- Multilevel Optimization ----------------------- ------------------------- 1. crude pre-optimization ------------------------- writing TMPCONF* Dirs from file "crest_rotamers_0.xyz" ... done. Starting optimization of generated structures 600 jobs to do. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 done. Now appending opt.xyz file with new structures running RMSDs... done. E lowest : -94.80531 537 structures remain within 12.00 kcal/mol window ------------------------------------- 2. optimization with tight thresholds ------------------------------------- writing TMPCONF* Dirs from file "crest_rotamers_1.xyz" ... done. Starting optimization of generated structures 538 jobs to do. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 done. Now appending opt.xyz file with new structures running RMSDs... done. E lowest : -94.80589 256 structures remain within 6.00 kcal/mol window ======================================== MTD Iterations done ======================================== Collecting ensmbles. running RMSDs... done. E lowest : -94.80589 260 structures remain within 6.00 kcal/mol window ----------------------------------------------- Additional regular MDs on lowest 4 conformer(s) ----------------------------------------------- Starting MD 3 with the settings: MD time /ps : 2.5 MD Temperature /K : 400.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 Starting MD 1 with the settings: MD time /ps : 2.5 MD Temperature /K : 400.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 Starting MD 2 with the settings: MD time /ps : 2.5 MD Temperature /K : 500.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 Starting MD 4 with the settings: MD time /ps : 2.5 MD Temperature /K : 500.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 Starting MD 5 with the settings: MD time /ps : 2.5 MD Temperature /K : 400.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 Starting MD 6 with the settings: MD time /ps : 2.5 MD Temperature /K : 500.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 Starting MD 7 with the settings: MD time /ps : 2.5 MD Temperature /K : 400.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 Starting MD 8 with the settings: MD time /ps : 2.5 MD Temperature /K : 500.0 dt /fs : 3.0 dumpstep(trj) /fs : 100 *MD 1 finished* *MD 2 finished* *MD 5 finished* *MD 3 finished* *MD 7 finished* *MD 4 finished* *MD 8 finished* *MD 6 finished* Appending file crest_rotamers_1.xyz with new structures ------------------------------------------- Ensemble optimization with tight thresholds ------------------------------------------- writing TMPCONF* Dirs from file "crest_rotamers_1.xyz" ... done. Starting optimization of generated structures 460 jobs to do. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 done. Now appending opt.xyz file with new structures running RMSDs... done. E lowest : -94.80589 283 structures remain within 6.00 kcal/mol window ======================================== | Structure Crossing (GC) | ======================================== ============================= # threads = 32 ============================= input file name : crest_rotamers_3.xyz number of atoms : 57 number of points on xyz files : 283 conformer energy window /kcal : 6.00 CN per atom difference cut-off : 0.3000 RMSD threshold : 0.2500 max. # of generated structures : 250 reading xyz file ... # in E window 283 generating pairs ... 40185 16.6 % done 57.2 % done generated pairs : 24395 number of clash discarded : 15508 average rmsd w.r.t input : 1.38507 sd of ensemble : 0.23227 number of new structures : 13 removed identical structures : 487 writing 13 TMPCONF* dirs ... -------------------------- GC: loose pre-optimization -------------------------- Starting optimization of generated structures 13 jobs to do. 1 2 3 4 5 6 7 8 9 10 11 12 13 done. Now appending opt.xyz file with new structures running RMSDs... done. E lowest : -94.79159 13 structures remain within 10.00 kcal/mol window -------------------------------------- GC: optimization with tight thresholds -------------------------------------- writing TMPCONF* Dirs from file "crest_rotamers_1.xyz" ... done. Starting optimization of generated structures 13 jobs to do. 1 2 3 4 5 6 7 8 9 10 11 12 13 done. Now appending opt.xyz file with new structures running RMSDs... done. E lowest : -94.80589 ================================================ | Final Geometry Optimization | ================================================ --------------------- Ensemble optimization --------------------- writing TMPCONF* Dirs from file "crest_rotamers_4.xyz" ... done. Starting optimization of generated structures 284 jobs to do. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 done. Now appending opt.xyz file with new structures running RMSDs... done. E lowest : -94.80589 279 structures remain within 6.00 kcal/mol window ------------------------------------- CREGEN - CONFORMER SYMMETRY ANALYSIS ------------------------------------- ============================= # threads = 32 ============================= input file name : crest_rotamers_5.xyz output file name : crest_rotamers_6.xyz number of atoms : 57 number of points on xyz files : 284 RMSD threshold : 0.1250 Bconst threshold : 15.0000 population threshold : 0.0500 conformer energy window /kcal : 6.0000 # fragment in coord : 1 number of reliable points : 284 reference state Etot : -94.8058891423000 number of doubles removed by rot/RMSD : 5 total number unique points considered further : 279 Erel/kcal Etot weight/tot conformer set degen origin 1 0.000 -94.80589 0.00466 0.99988 1 215 mtd9 2 0.000 -94.80589 0.00466 mtd3 3 0.000 -94.80589 0.00466 mtd5 4 0.000 -94.80589 0.00466 md4 5 0.000 -94.80589 0.00466 md7 6 0.000 -94.80589 0.00466 md7 7 0.000 -94.80589 0.00466 md8 8 0.000 -94.80589 0.00466 mtd1 9 0.000 -94.80589 0.00466 mtd8 10 0.000 -94.80589 0.00466 mtd9 11 0.000 -94.80589 0.00466 md8 12 0.000 -94.80589 0.00466 md5 13 0.000 -94.80589 0.00466 md5 14 0.000 -94.80589 0.00466 mtd5 15 0.000 -94.80589 0.00466 mtd10 16 0.000 -94.80589 0.00466 mtd12 17 0.000 -94.80589 0.00466 mtd3 18 0.000 -94.80589 0.00466 md3 19 0.000 -94.80589 0.00466 mtd2 20 0.000 -94.80589 0.00466 mtd2 21 0.000 -94.80589 0.00466 mtd10 22 0.000 -94.80589 0.00466 mtd3 23 0.000 -94.80589 0.00466 md7 24 0.000 -94.80589 0.00466 mtd3 25 0.000 -94.80589 0.00466 md3 26 0.000 -94.80589 0.00466 mtd6 27 0.000 -94.80589 0.00466 md6 28 0.000 -94.80589 0.00466 md1 29 0.000 -94.80589 0.00466 mtd3 30 0.000 -94.80589 0.00466 mtd1 31 0.000 -94.80589 0.00466 mtd8 32 0.000 -94.80589 0.00466 mtd1 33 0.000 -94.80589 0.00466 mtd1 34 0.000 -94.80589 0.00466 mtd11 35 0.000 -94.80589 0.00466 mtd2 36 0.000 -94.80589 0.00466 mtd5 37 0.000 -94.80589 0.00466 mtd3 38 0.000 -94.80589 0.00466 md4 39 0.000 -94.80589 0.00466 mtd2 40 0.000 -94.80589 0.00466 mtd1 41 0.000 -94.80589 0.00466 mtd9 42 0.001 -94.80589 0.00466 mtd12 43 0.001 -94.80589 0.00466 md6 44 0.001 -94.80589 0.00466 mtd1 45 0.001 -94.80589 0.00466 mtd5 46 0.001 -94.80589 0.00466 mtd3 47 0.001 -94.80589 0.00466 mtd9 48 0.001 -94.80589 0.00466 mtd9 49 0.001 -94.80589 0.00466 mtd1 50 0.001 -94.80589 0.00466 mtd5 51 0.001 -94.80589 0.00466 mtd9 52 0.001 -94.80589 0.00466 mtd3 53 0.001 -94.80589 0.00466 mtd5 54 0.001 -94.80589 0.00466 mtd1 55 0.001 -94.80589 0.00466 mtd3 56 0.001 -94.80589 0.00466 mtd9 57 0.001 -94.80589 0.00466 mtd4 58 0.001 -94.80589 0.00466 mtd4 59 0.001 -94.80589 0.00466 mtd5 60 0.001 -94.80589 0.00466 mtd2 61 0.001 -94.80589 0.00466 mtd9 62 0.001 -94.80589 0.00466 mtd9 63 0.001 -94.80589 0.00466 mtd3 64 0.001 -94.80589 0.00466 md4 65 0.001 -94.80589 0.00466 md2 66 0.001 -94.80589 0.00466 mtd12 67 0.001 -94.80589 0.00466 md7 68 0.001 -94.80589 0.00466 mtd1 69 0.001 -94.80589 0.00465 md4 70 0.001 -94.80589 0.00465 mtd4 71 0.001 -94.80589 0.00465 md5 72 0.001 -94.80589 0.00465 mtd4 73 0.001 -94.80589 0.00465 mtd1 74 0.001 -94.80589 0.00465 md7 75 0.001 -94.80589 0.00465 mtd1 76 0.001 -94.80589 0.00465 mtd5 77 0.001 -94.80589 0.00465 md8 78 0.001 -94.80589 0.00465 mtd2 79 0.001 -94.80589 0.00465 mtd4 80 0.001 -94.80589 0.00465 mtd12 81 0.001 -94.80589 0.00465 mtd2 82 0.001 -94.80589 0.00465 mtd1 83 0.001 -94.80589 0.00465 md6 84 0.001 -94.80589 0.00465 md5 85 0.001 -94.80589 0.00465 mtd1 86 0.001 -94.80589 0.00465 md6 87 0.001 -94.80589 0.00465 md8 88 0.001 -94.80589 0.00465 md1 89 0.001 -94.80589 0.00465 mtd5 90 0.001 -94.80589 0.00465 mtd4 91 0.001 -94.80589 0.00465 mtd6 92 0.001 -94.80589 0.00465 mtd9 93 0.001 -94.80589 0.00465 gc 94 0.001 -94.80589 0.00465 mtd6 95 0.001 -94.80589 0.00465 mtd2 96 0.001 -94.80589 0.00465 md7 97 0.001 -94.80589 0.00465 md4 98 0.001 -94.80589 0.00465 mtd5 99 0.001 -94.80589 0.00465 mtd1 100 0.001 -94.80589 0.00465 mtd7 101 0.001 -94.80589 0.00465 mtd7 102 0.001 -94.80589 0.00465 mtd3 103 0.001 -94.80589 0.00465 mtd3 104 0.001 -94.80589 0.00465 md3 105 0.001 -94.80589 0.00465 md1 106 0.001 -94.80589 0.00465 mtd3 107 0.001 -94.80589 0.00465 mtd9 108 0.001 -94.80589 0.00465 mtd3 109 0.001 -94.80589 0.00465 mtd12 110 0.001 -94.80589 0.00465 md4 111 0.001 -94.80589 0.00465 mtd8 112 0.001 -94.80589 0.00465 mtd4 113 0.001 -94.80589 0.00465 md1 114 0.001 -94.80589 0.00465 md5 115 0.001 -94.80589 0.00465 md5 116 0.001 -94.80589 0.00465 mtd1 117 0.001 -94.80589 0.00465 md6 118 0.001 -94.80589 0.00465 mtd3 119 0.001 -94.80589 0.00465 md3 120 0.001 -94.80589 0.00465 md2 121 0.001 -94.80589 0.00465 mtd2 122 0.001 -94.80589 0.00465 mtd2 123 0.001 -94.80589 0.00465 mtd8 124 0.001 -94.80589 0.00465 mtd3 125 0.001 -94.80589 0.00465 mtd3 126 0.001 -94.80589 0.00465 mtd6 127 0.001 -94.80589 0.00465 mtd8 128 0.001 -94.80589 0.00465 mtd1 129 0.001 -94.80589 0.00465 md6 130 0.001 -94.80589 0.00465 mtd5 131 0.001 -94.80589 0.00465 mtd8 132 0.001 -94.80589 0.00465 mtd8 133 0.001 -94.80589 0.00465 md8 134 0.001 -94.80589 0.00465 gc 135 0.001 -94.80589 0.00465 gc 136 0.001 -94.80589 0.00465 mtd6 137 0.001 -94.80589 0.00465 mtd6 138 0.001 -94.80589 0.00465 md4 139 0.001 -94.80589 0.00465 mtd8 140 0.001 -94.80589 0.00465 mtd3 141 0.001 -94.80589 0.00465 md2 142 0.001 -94.80589 0.00465 mtd4 143 0.001 -94.80589 0.00465 md8 144 0.001 -94.80589 0.00465 md4 145 0.001 -94.80589 0.00465 md6 146 0.001 -94.80589 0.00465 mtd3 147 0.001 -94.80589 0.00465 mtd2 148 0.001 -94.80589 0.00465 gc 149 0.001 -94.80589 0.00465 md6 150 0.001 -94.80589 0.00465 mtd9 151 0.001 -94.80589 0.00465 mtd3 152 0.001 -94.80589 0.00465 md7 153 0.001 -94.80589 0.00465 md8 154 0.001 -94.80589 0.00465 md4 155 0.002 -94.80589 0.00465 md5 156 0.002 -94.80589 0.00465 mtd6 157 0.002 -94.80589 0.00465 mtd1 158 0.002 -94.80589 0.00465 md6 159 0.002 -94.80589 0.00465 mtd3 160 0.002 -94.80589 0.00465 mtd8 161 0.002 -94.80589 0.00465 mtd8 162 0.002 -94.80589 0.00465 mtd2 163 0.002 -94.80589 0.00465 mtd3 164 0.002 -94.80589 0.00465 mtd1 165 0.002 -94.80589 0.00465 mtd11 166 0.002 -94.80589 0.00465 mtd2 167 0.002 -94.80589 0.00465 mtd8 168 0.002 -94.80589 0.00465 mtd11 169 0.002 -94.80589 0.00465 mtd8 170 0.002 -94.80589 0.00465 mtd8 171 0.002 -94.80589 0.00465 mtd8 172 0.002 -94.80589 0.00465 mtd9 173 0.002 -94.80589 0.00465 mtd2 174 0.002 -94.80589 0.00465 mtd4 175 0.002 -94.80589 0.00465 mtd2 176 0.002 -94.80589 0.00465 mtd2 177 0.002 -94.80589 0.00465 md5 178 0.002 -94.80589 0.00465 md7 179 0.002 -94.80589 0.00464 mtd6 180 0.002 -94.80589 0.00464 mtd10 181 0.002 -94.80589 0.00464 mtd7 182 0.002 -94.80589 0.00464 md8 183 0.002 -94.80589 0.00464 mtd8 184 0.002 -94.80589 0.00464 mtd3 185 0.002 -94.80589 0.00464 md4 186 0.002 -94.80589 0.00464 mtd4 187 0.002 -94.80589 0.00464 mtd12 188 0.002 -94.80589 0.00464 md7 189 0.002 -94.80589 0.00464 mtd5 190 0.002 -94.80589 0.00464 mtd3 191 0.002 -94.80589 0.00464 md2 192 0.002 -94.80589 0.00464 mtd2 193 0.002 -94.80589 0.00464 md1 194 0.002 -94.80589 0.00464 mtd6 195 0.002 -94.80589 0.00464 md7 196 0.003 -94.80589 0.00464 mtd1 197 0.003 -94.80589 0.00464 mtd5 198 0.003 -94.80588 0.00464 mtd8 199 0.003 -94.80588 0.00464 mtd10 200 0.003 -94.80588 0.00464 mtd4 201 0.003 -94.80588 0.00464 md4 202 0.003 -94.80588 0.00464 mtd2 203 0.003 -94.80588 0.00464 md4 204 0.003 -94.80588 0.00464 mtd8 205 0.003 -94.80588 0.00464 mtd8 206 0.003 -94.80588 0.00464 md4 207 0.003 -94.80588 0.00464 mtd3 208 0.004 -94.80588 0.00463 mtd5 209 0.004 -94.80588 0.00463 md7 210 0.004 -94.80588 0.00463 mtd3 211 0.005 -94.80588 0.00463 mtd12 212 0.005 -94.80588 0.00462 mtd1 213 0.005 -94.80588 0.00462 mtd1 214 0.006 -94.80588 0.00461 mtd11 215 0.006 -94.80588 0.00461 mtd9 216 4.274 -94.79908 0.00000 0.00001 2 2 mtd10 217 4.278 -94.79907 0.00000 mtd10 218 4.540 -94.79865 0.00000 0.00009 3 42 mtd5 219 4.540 -94.79865 0.00000 mtd5 220 4.540 -94.79865 0.00000 mtd5 221 4.540 -94.79865 0.00000 mtd10 222 4.540 -94.79865 0.00000 mtd5 223 4.541 -94.79865 0.00000 mtd4 224 4.541 -94.79865 0.00000 mtd9 225 4.541 -94.79865 0.00000 mtd7 226 4.541 -94.79865 0.00000 mtd2 227 4.541 -94.79865 0.00000 mtd9 228 4.541 -94.79865 0.00000 mtd11 229 4.541 -94.79865 0.00000 mtd2 230 4.541 -94.79865 0.00000 mtd5 231 4.541 -94.79865 0.00000 mtd4 232 4.542 -94.79865 0.00000 mtd7 233 4.542 -94.79865 0.00000 mtd5 234 4.542 -94.79865 0.00000 mtd4 235 4.542 -94.79865 0.00000 mtd9 236 4.542 -94.79865 0.00000 mtd2 237 4.542 -94.79865 0.00000 mtd11 238 4.542 -94.79865 0.00000 mtd11 239 4.542 -94.79865 0.00000 mtd10 240 4.542 -94.79865 0.00000 mtd7 241 4.542 -94.79865 0.00000 mtd10 242 4.542 -94.79865 0.00000 mtd2 243 4.542 -94.79865 0.00000 mtd5 244 4.543 -94.79865 0.00000 mtd7 245 4.543 -94.79865 0.00000 mtd9 246 4.543 -94.79865 0.00000 mtd5 247 4.543 -94.79865 0.00000 mtd2 248 4.543 -94.79865 0.00000 mtd9 249 4.544 -94.79865 0.00000 mtd9 250 4.544 -94.79865 0.00000 mtd11 251 4.545 -94.79865 0.00000 mtd5 252 4.545 -94.79865 0.00000 mtd9 253 4.545 -94.79865 0.00000 mtd9 254 4.546 -94.79864 0.00000 mtd2 255 4.547 -94.79864 0.00000 mtd7 256 4.547 -94.79864 0.00000 mtd4 257 4.551 -94.79864 0.00000 mtd2 258 4.554 -94.79863 0.00000 mtd2 259 4.557 -94.79863 0.00000 mtd2 260 4.730 -94.79835 0.00000 0.00001 4 6 mtd4 261 4.731 -94.79835 0.00000 mtd4 262 4.731 -94.79835 0.00000 mtd11 263 4.732 -94.79835 0.00000 mtd11 264 4.732 -94.79835 0.00000 mtd4 265 4.732 -94.79835 0.00000 mtd4 266 5.207 -94.79759 0.00000 0.00000 5 5 mtd4 267 5.208 -94.79759 0.00000 mtd4 268 5.208 -94.79759 0.00000 mtd4 269 5.209 -94.79759 0.00000 mtd4 270 5.209 -94.79759 0.00000 mtd4 271 5.251 -94.79752 0.00000 0.00001 6 8 mtd4 272 5.257 -94.79751 0.00000 mtd11 273 5.257 -94.79751 0.00000 mtd11 274 5.258 -94.79751 0.00000 mtd11 275 5.258 -94.79751 0.00000 mtd11 276 5.258 -94.79751 0.00000 mtd11 277 5.258 -94.79751 0.00000 mtd11 278 5.259 -94.79751 0.00000 mtd11 279 5.896 -94.79649 0.00000 0.00000 7 1 mtd10 T /K : 298.15 E lowest : -94.80589 ensemble average energy (kcal) : 0.002 ensemble entropy (J/mol K, cal/mol K) : 44.663 10.675 ensemble free energy (kcal/mol) : -3.183 population of lowest in % : 99.988 number of unique conformers for further calc 7 list of relative energies saved as "crest.energies" Normal termination. ----------------- Wall Time Summary ----------------- test MD wall time : 0h : 3m :21s MTD wall time : 0h :23m : 5s multilevel OPT wall time : 0h :20m :45s MD wall time : 0h : 8m :52s GC wall time : 0h : 0m :49s -------------------- Overall wall time : 0h :59m :19s CREST terminated normally.