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==============================================
| |
| 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:
> crest OPT.xyz -opt vtight -T 8
-opt 2
-T 8 (CPUs/Threads selected)
-------------------------
Starting z-matrix sorting
-------------------------
total number of atoms : 23
total number of frags : 1
Fragment 1
1 C 0.000000 0.0000 0.0000 0 0 0
2 O 2.654097 0.0000 0.0000 1 0 0
3 H 1.875498 107.0976 0.0000 2 1 0
4 C 2.938240 111.6638 -92.6636 1 2 3
5 C 2.937875 108.3730 -178.6152 4 1 2
6 O 2.654363 111.6105 -178.4277 5 4 1
7 H 1.875457 107.1737 -93.5006 6 5 4
8 H 2.096529 108.0491 -122.1549 5 6 4
9 H 2.107646 110.4420 -113.9181 5 6 8
10 C 2.939065 109.6605 -119.1647 4 5 1
11 O 2.655133 111.7344 -299.3321 10 4 5
12 H 1.875542 107.2090 -94.5646 11 10 4
13 H 2.099975 107.7972 -121.4065 10 11 4
14 H 2.108029 110.3904 -114.5674 10 11 13
15 C 2.954992 107.6775 -239.3642 4 10 5
16 C 2.897805 115.7522 -180.1590 15 4 10
17 H 2.094612 111.3728 -61.1660 16 15 4
18 H 2.094665 111.3556 -237.2970 16 15 17
19 H 2.098442 109.0501 -118.6998 16 15 17
20 H 2.101352 107.5877 -237.4034 15 16 4
21 H 2.101761 107.5214 -245.0594 15 16 20
22 H 2.099809 110.2637 -240.1080 1 4 2
23 H 2.105075 111.4734 -244.0028 1 4 22
terminated normally
-------------------------
xTB Geometry Optimization
-------------------------
Geometry successfully optimized.
------------------------------------------------
Generating MTD length from a flexibility measure
------------------------------------------------
Calculating WBOs... done.
flexibility measure : 0.706
t(MTD) / ps : 5.0
Σ(t(MTD)) / ps : 60.0 (+ 10.0)
-------------------------------------
Starting a trial MTD to test settings
-------------------------------------
Estimated runtime for one MTD (5.0 ps) on a single thread: 1 min 40 sec
Estimated runtime for a batch of 14 MTDs on 8 threads: 3 min 19 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 1 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0690
Vbias exponent(α) : 1.30
Starting Meta-MD 4 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0690
Vbias exponent(α) : 0.78
Starting Meta-MD 2 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0345
Vbias exponent(α) : 1.30
Starting Meta-MD 3 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0173
Vbias exponent(α) : 1.30
Starting Meta-MD 6 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0173
Vbias exponent(α) : 0.78
Starting Meta-MD 5 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0345
Vbias exponent(α) : 0.78
Starting Meta-MD 7 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0690
Vbias exponent(α) : 0.47
Starting Meta-MD 14 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.1150
Vbias exponent(α) : 0.80
*Meta-MD 2 finished*
Starting Meta-MD 8 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0345
Vbias exponent(α) : 0.47
*Meta-MD 3 finished*
Starting Meta-MD 9 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
*Meta-MD 5 finished*
dumpstep(trj) /fs : 100
*Meta-MD 1 finished*
dumpstep(Vbias)/ps : 1.0
*Meta-MD 7 finished*
Vbias prefactor(k) : 0.0173
Vbias exponent(α) : 0.47
Starting Meta-MD 10 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0690
Vbias exponent(α) : 0.28
Starting Meta-MD 11 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0345
Vbias exponent(α) : 0.28
Starting Meta-MD 12 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0173
Vbias exponent(α) : 0.28
*Meta-MD 14 finished*
Starting Meta-MD 13 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0230
Vbias exponent(α) : 0.10
*Meta-MD 4 finished*
*Meta-MD 6 finished*
*Meta-MD 11 finished*
*Meta-MD 12 finished*
*Meta-MD 13 finished*
*Meta-MD 8 finished*
*Meta-MD 10 finished*
*Meta-MD 9 finished*
-----------------------
Multilevel Optimization
-----------------------
-------------------------
1. crude pre-optimization
-------------------------
writing TMPCONF* Dirs from file "crest_rotamers_0.xyz" ... done.
Starting optimization of generated structures
686 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
done.
Now appending opt.xyz file with new structures
running RMSDs...
done.
E lowest : -32.17988
579 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
580 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
done.
Now appending opt.xyz file with new structures
running RMSDs...
done.
E lowest : -32.18006
114 structures remain within 6.00 kcal/mol window
========================================
MTD Iteration 2
========================================
========================================
| Meta-MD (MTD) Sampling |
========================================
Starting Meta-MD 4 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0690
Vbias exponent(α) : 0.78
Starting Meta-MD 3 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0173
Vbias exponent(α) : 1.30
Starting Meta-MD 1 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0690
Vbias exponent(α) : 1.30
Starting Meta-MD 5 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0345
Vbias exponent(α) : 0.78
Starting Meta-MD 2 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0345
Vbias exponent(α) : 1.30
Starting Meta-MD 6 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0173
Vbias exponent(α) : 0.78
Starting Meta-MD 7 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0690
Vbias exponent(α) : 0.47
Starting Meta-MD 12 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0173
Vbias exponent(α) : 0.28
*Meta-MD 7 finished*
*Meta-MD 12 finished*
*Meta-MD 5 finished*
Starting Meta-MD 8 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
*Meta-MD 3 finished*
*Meta-MD 1 finished*
Vbias prefactor(k) : 0.0345
*Meta-MD 2 finished*
Vbias exponent(α) : 0.47
Starting Meta-MD 11 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0345
Vbias exponent(α) : 0.28
Starting Meta-MD 9 with the settings:
MD time /ps : 5.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0173
Vbias exponent(α) : 0.47
Starting Meta-MD 10 with the settings:
MD time /ps : 5.0
*Meta-MD 6 finished*
dt /fs : 5.0
dumpstep(trj) /fs : 100
dumpstep(Vbias)/ps : 1.0
Vbias prefactor(k) : 0.0690
*Meta-MD 4 finished*
Vbias exponent(α) : 0.28
*Meta-MD 9 finished*
*Meta-MD 11 finished*
*Meta-MD 10 finished*
*Meta-MD 8 finished*
-----------------------
Multilevel Optimization
-----------------------
-------------------------
1. crude pre-optimization
-------------------------
writing TMPCONF* Dirs from file "crest_rotamers_0.xyz" ... done.
Starting optimization of generated structures
588 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
done.
Now appending opt.xyz file with new structures
running RMSDs...
done.
E lowest : -32.18000
342 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
343 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
done.
Now appending opt.xyz file with new structures
running RMSDs...
done.
E lowest : -32.18006
68 structures remain within 6.00 kcal/mol window
========================================
MTD Iterations done
========================================
Collecting ensmbles.
running RMSDs...
done.
E lowest : -32.18006
170 structures remain within 6.00 kcal/mol window
-----------------------------------------------
Additional regular MDs on lowest 4 conformer(s)
-----------------------------------------------
Starting MD 2 with the settings:
MD time /ps : 2.5
MD Temperature /K : 500.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
Starting MD 1 with the settings:
MD time /ps : 2.5
MD Temperature /K : 400.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
Starting MD 3 with the settings:
MD time /ps : 2.5
MD Temperature /K : 400.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
Starting MD 8 with the settings:
MD time /ps : 2.5
MD Temperature /K : 500.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
Starting MD 4 with the settings:
MD time /ps : 2.5
MD Temperature /K : 500.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
Starting MD 5 with the settings:
MD time /ps : 2.5
MD Temperature /K : 400.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
Starting MD 6 with the settings:
MD time /ps : 2.5
MD Temperature /K : 500.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
Starting MD 7 with the settings:
MD time /ps : 2.5
MD Temperature /K : 400.0
dt /fs : 5.0
dumpstep(trj) /fs : 100
*MD 1 finished*
*MD 2 finished*
*MD 4 finished*
*MD 7 finished*
*MD 6 finished*
*MD 8 finished*
*MD 3 finished*
*MD 5 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
362 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
done.
Now appending opt.xyz file with new structures
running RMSDs...
done.
E lowest : -32.18006
176 structures remain within 6.00 kcal/mol window
========================================
| Structure Crossing (GC) |
========================================
=============================
# threads = 8
=============================
input file name : crest_rotamers_3.xyz
number of atoms : 23
number of points on xyz files : 176
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 176
generating pairs ... 15575
60.8 % done
generated pairs : 15218
number of clash discarded : 182
average rmsd w.r.t input : 2.95474
sd of ensemble : 0.61186
number of new structures : 155
removed identical structures : 345
writing 155 TMPCONF* dirs ...
--------------------------
GC: loose pre-optimization
--------------------------
Starting optimization of generated structures
155 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
done.
Now appending opt.xyz file with new structures
running RMSDs...
done.
E lowest : -32.18005
70 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
70 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
done.
Now appending opt.xyz file with new structures
running RMSDs...
done.
E lowest : -32.18006
================================================
| Final Geometry Optimization |
================================================
---------------------
Ensemble optimization
---------------------
writing TMPCONF* Dirs from file "crest_rotamers_4.xyz" ... done.
Starting optimization of generated structures
184 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
done.
Now appending opt.xyz file with new structures
running RMSDs...
done.
E lowest : -32.18006
182 structures remain within 6.00 kcal/mol window
-------------------------------------
CREGEN - CONFORMER SYMMETRY ANALYSIS
-------------------------------------
=============================
# threads = 8
=============================
input file name : crest_rotamers_5.xyz
output file name : crest_rotamers_6.xyz
number of atoms : 23
number of points on xyz files : 184
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 : 184
reference state Etot : -32.1800611637000
number of doubles removed by rot/RMSD : 2
total number unique points considered further : 182
Erel/kcal Etot weight/tot conformer set degen origin
1 0.000 -32.18006 0.06606 0.99057 1 15 mtd1
2 0.000 -32.18006 0.06606 mtd5
3 0.000 -32.18006 0.06605 mtd2
4 0.000 -32.18006 0.06605 mtd2
5 0.000 -32.18006 0.06605 mtd1
6 0.000 -32.18006 0.06605 mtd3
7 0.000 -32.18006 0.06604 md1
8 0.000 -32.18006 0.06604 mtd5
9 0.000 -32.18006 0.06604 md1
10 0.000 -32.18006 0.06604 gc
11 0.000 -32.18006 0.06603 mtd11
12 0.000 -32.18006 0.06603 md2
13 0.000 -32.18006 0.06603 mtd3
14 0.000 -32.18006 0.06602 mtd11
15 0.001 -32.18006 0.06599 md1
16 3.312 -32.17478 0.00025 0.00272 2 11 gc
17 3.312 -32.17478 0.00025 md3
18 3.312 -32.17478 0.00025 mtd10
19 3.313 -32.17478 0.00025 mtd3
20 3.313 -32.17478 0.00025 mtd7
21 3.313 -32.17478 0.00025 gc
22 3.313 -32.17478 0.00025 gc
23 3.313 -32.17478 0.00025 gc
24 3.313 -32.17478 0.00025 mtd11
25 3.313 -32.17478 0.00025 mtd1
26 3.313 -32.17478 0.00025 gc
27 3.386 -32.17467 0.00022 0.00263 3 12 md6
28 3.386 -32.17467 0.00022 mtd1
29 3.386 -32.17467 0.00022 mtd1
30 3.386 -32.17467 0.00022 mtd9
31 3.386 -32.17467 0.00022 mtd1
32 3.386 -32.17467 0.00022 mtd7
33 3.386 -32.17467 0.00022 mtd9
34 3.386 -32.17467 0.00022 mtd6
35 3.386 -32.17467 0.00022 mtd5
36 3.386 -32.17467 0.00022 mtd9
37 3.387 -32.17466 0.00022 mtd3
38 3.387 -32.17466 0.00022 gc
39 3.636 -32.17427 0.00014 0.00158 4 11 mtd10
40 3.636 -32.17427 0.00014 md7
41 3.636 -32.17427 0.00014 mtd11
42 3.636 -32.17427 0.00014 mtd4
43 3.636 -32.17427 0.00014 mtd9
44 3.636 -32.17427 0.00014 mtd10
45 3.636 -32.17427 0.00014 mtd7
46 3.636 -32.17427 0.00014 gc
47 3.636 -32.17427 0.00014 mtd4
48 3.637 -32.17427 0.00014 mtd6
49 3.637 -32.17427 0.00014 mtd6
50 4.274 -32.17325 0.00005 0.00044 5 9 mtd8
51 4.274 -32.17325 0.00005 mtd3
52 4.274 -32.17325 0.00005 mtd3
53 4.274 -32.17325 0.00005 gc
54 4.275 -32.17325 0.00005 mtd13
55 4.275 -32.17325 0.00005 mtd9
56 4.275 -32.17325 0.00005 mtd12
57 4.275 -32.17325 0.00005 mtd7
58 4.275 -32.17325 0.00005 gc
59 4.438 -32.17299 0.00004 0.00019 6 5 mtd12
60 4.438 -32.17299 0.00004 mtd9
61 4.438 -32.17299 0.00004 mtd9
62 4.438 -32.17299 0.00004 mtd11
63 4.439 -32.17299 0.00004 mtd3
64 4.499 -32.17289 0.00003 0.00030 7 9 md6
65 4.499 -32.17289 0.00003 mtd12
66 4.499 -32.17289 0.00003 mtd9
67 4.499 -32.17289 0.00003 mtd1
68 4.499 -32.17289 0.00003 mtd1
69 4.499 -32.17289 0.00003 mtd6
70 4.499 -32.17289 0.00003 gc
71 4.499 -32.17289 0.00003 mtd10
72 4.500 -32.17289 0.00003 mtd13
73 4.511 -32.17287 0.00003 0.00016 8 5 mtd12
74 4.511 -32.17287 0.00003 mtd10
75 4.511 -32.17287 0.00003 gc
76 4.511 -32.17287 0.00003 mtd4
77 4.511 -32.17287 0.00003 mtd6
78 4.608 -32.17272 0.00003 0.00022 9 8 mtd4
79 4.609 -32.17272 0.00003 mtd10
80 4.609 -32.17272 0.00003 mtd3
81 4.609 -32.17272 0.00003 mtd3
82 4.609 -32.17272 0.00003 mtd3
83 4.609 -32.17272 0.00003 mtd12
84 4.609 -32.17272 0.00003 mtd8
85 4.610 -32.17271 0.00003 mtd10
86 4.625 -32.17269 0.00003 0.00016 10 6 mtd7
87 4.625 -32.17269 0.00003 md8
88 4.625 -32.17269 0.00003 mtd7
89 4.625 -32.17269 0.00003 mtd6
90 4.625 -32.17269 0.00003 mtd7
91 4.625 -32.17269 0.00003 mtd10
92 4.694 -32.17258 0.00002 0.00019 11 8 mtd12
93 4.694 -32.17258 0.00002 mtd10
94 4.694 -32.17258 0.00002 md8
95 4.694 -32.17258 0.00002 mtd11
96 4.694 -32.17258 0.00002 mtd3
97 4.694 -32.17258 0.00002 mtd4
98 4.695 -32.17258 0.00002 mtd12
99 4.695 -32.17258 0.00002 mtd8
100 4.709 -32.17256 0.00002 0.00007 12 3 mtd7
101 4.709 -32.17256 0.00002 mtd4
102 4.709 -32.17256 0.00002 mtd1
103 4.743 -32.17250 0.00002 0.00016 13 7 mtd7
104 4.743 -32.17250 0.00002 mtd11
105 4.743 -32.17250 0.00002 mtd3
106 4.743 -32.17250 0.00002 mtd14
107 4.743 -32.17250 0.00002 mtd12
108 4.743 -32.17250 0.00002 mtd1
109 4.743 -32.17250 0.00002 mtd12
110 4.766 -32.17247 0.00002 0.00004 14 2 mtd14
111 4.767 -32.17246 0.00002 mtd12
112 4.780 -32.17244 0.00002 0.00004 15 2 mtd3
113 4.782 -32.17244 0.00002 mtd8
114 4.832 -32.17236 0.00002 0.00013 16 7 md7
115 4.832 -32.17236 0.00002 mtd4
116 4.832 -32.17236 0.00002 mtd7
117 4.832 -32.17236 0.00002 gc
118 4.832 -32.17236 0.00002 mtd6
119 4.832 -32.17236 0.00002 mtd4
120 4.832 -32.17236 0.00002 mtd4
121 5.055 -32.17200 0.00001 0.00007 17 5 mtd8
122 5.055 -32.17200 0.00001 mtd5
123 5.055 -32.17200 0.00001 mtd5
124 5.056 -32.17200 0.00001 mtd4
125 5.056 -32.17200 0.00001 mtd5
126 5.097 -32.17194 0.00001 0.00004 18 3 mtd3
127 5.098 -32.17194 0.00001 mtd5
128 5.098 -32.17194 0.00001 mtd9
129 5.106 -32.17192 0.00001 0.00008 19 7 mtd2
130 5.106 -32.17192 0.00001 mtd4
131 5.106 -32.17192 0.00001 mtd11
132 5.106 -32.17192 0.00001 mtd11
133 5.106 -32.17192 0.00001 mtd2
134 5.107 -32.17192 0.00001 mtd2
135 5.107 -32.17192 0.00001 mtd2
136 5.305 -32.17161 0.00001 0.00004 20 5 mtd11
137 5.306 -32.17161 0.00001 mtd8
138 5.306 -32.17161 0.00001 mtd11
139 5.306 -32.17161 0.00001 mtd4
140 5.306 -32.17161 0.00001 mtd11
141 5.314 -32.17159 0.00001 0.00003 21 3 mtd13
142 5.314 -32.17159 0.00001 mtd8
143 5.314 -32.17159 0.00001 mtd4
144 5.638 -32.17108 0.00000 0.00001 22 2 mtd7
145 5.638 -32.17108 0.00000 mtd10
146 5.680 -32.17101 0.00000 0.00001 23 3 mtd9
147 5.680 -32.17101 0.00000 mtd7
148 5.680 -32.17101 0.00000 mtd7
149 5.699 -32.17098 0.00000 0.00003 24 7 mtd7
150 5.699 -32.17098 0.00000 mtd7
151 5.699 -32.17098 0.00000 mtd10
152 5.699 -32.17098 0.00000 mtd9
153 5.699 -32.17098 0.00000 mtd12
154 5.699 -32.17098 0.00000 mtd3
155 5.700 -32.17098 0.00000 mtd10
156 5.744 -32.17091 0.00000 0.00001 25 2 mtd8
157 5.744 -32.17091 0.00000 mtd2
158 5.820 -32.17079 0.00000 0.00001 26 3 mtd7
159 5.821 -32.17079 0.00000 mtd5
160 5.821 -32.17079 0.00000 mtd1
161 5.896 -32.17067 0.00000 0.00000 27 1 mtd4
162 5.917 -32.17063 0.00000 0.00002 28 5 mtd7
163 5.917 -32.17063 0.00000 mtd11
164 5.917 -32.17063 0.00000 mtd5
165 5.917 -32.17063 0.00000 mtd5
166 5.917 -32.17063 0.00000 mtd9
167 5.943 -32.17059 0.00000 0.00001 29 5 md6
168 5.944 -32.17059 0.00000 mtd10
169 5.944 -32.17059 0.00000 mtd1
170 5.944 -32.17059 0.00000 mtd6
171 5.944 -32.17059 0.00000 mtd1
172 5.962 -32.17056 0.00000 0.00001 30 4 mtd10
173 5.962 -32.17056 0.00000 mtd7
174 5.962 -32.17056 0.00000 mtd9
175 5.962 -32.17056 0.00000 mtd8
176 5.997 -32.17050 0.00000 0.00001 31 3 mtd5
177 5.997 -32.17050 0.00000 mtd2
178 5.997 -32.17050 0.00000 mtd8
179 5.997 -32.17050 0.00000 0.00001 32 4 mtd10
180 5.997 -32.17050 0.00000 mtd2
181 5.998 -32.17050 0.00000 mtd5
182 5.998 -32.17050 0.00000 mtd2
T /K : 298.15
E lowest : -32.18006
ensemble average energy (kcal) : 0.036
ensemble entropy (J/mol K, cal/mol K) : 23.091 5.519
ensemble free energy (kcal/mol) : -1.645
population of lowest in % : 99.057
number of unique conformers for further calc 32
list of relative energies saved as "crest.energies"
Normal termination.
-----------------
Wall Time Summary
-----------------
test MD wall time : 0h : 0m : 2s
MTD wall time : 0h : 1m :55s
multilevel OPT wall time : 0h : 4m :27s
MD wall time : 0h : 0m :56s
GC wall time : 0h : 0m :33s
--------------------
Overall wall time : 0h : 8m :13s
CREST terminated normally.