PLUMED: PLUMED is starting
PLUMED: Version: 2.10.1 (git: f913f7678) compiled on Jul 27 2026 at 12:48:58
PLUMED: Please cite these papers when using PLUMED [1][2]
PLUMED: For further information see the PLUMED web page at http://www.plumed.org
PLUMED: Root: /home/runner/opt/lib/plumed
PLUMED: LibraryPath: /home/runner/opt/lib/libplumedKernel.so
PLUMED: For installed feature, see /home/runner/opt/lib/plumed/src/config/config.txt
PLUMED: Molecular dynamics engine: driver
PLUMED: Precision of reals: 8
PLUMED: Running over 1 node
PLUMED: Number of threads: 1
PLUMED: Cache line size: 512
PLUMED: Number of atoms: 100000
PLUMED: File suffix: 
PLUMED: FILE: plumed.dat
PLUMED: Action UNITS
PLUMED:   with label @0
PLUMED:   length: A = 0.1 nm
PLUMED:   energy: kj/mol
PLUMED:   time: 0.001 ps
PLUMED:   charge: e
PLUMED:   mass: amu
PLUMED:   using physical units
PLUMED:   inside PLUMED, Boltzmann constant is 0.00831446
PLUMED: Action GROUP
PLUMED:   with label Na
PLUMED:   list of atoms:
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  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
PLUMED:  701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725
PLUMED:  726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750
PLUMED:  751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775
PLUMED:  776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800
PLUMED:  801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825
PLUMED:  826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850
PLUMED:  851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875
PLUMED:  876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900
PLUMED:  901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925
PLUMED:  926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950
PLUMED:  951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975
PLUMED:  976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000
PLUMED: Action GROUP
PLUMED:   with label N
PLUMED:   list of atoms:
PLUMED:  1001
PLUMED: Action GROUP
PLUMED:   with label H
PLUMED:   list of atoms:
PLUMED:  1002 1003 1004
PLUMED: Action DISTANCES
PLUMED:   with label dnh
PLUMED: Action DISTANCE
PLUMED:   with label dnh
PLUMED:   between atoms 1001 1002
PLUMED:   between atoms 1001 1003
PLUMED:   between atoms 1001 1004
PLUMED:   using periodic boundary conditions
PLUMED: Action CUSTOM
PLUMED:   with label dnh_me_min
PLUMED:   with arguments : 
PLUMED:    vector with label dnh 
PLUMED:   with function : exp(20.0/x)
PLUMED:   with variables : x
PLUMED:   function as parsed by lepton: exp((20)/(x))
PLUMED:   derivatives as computed by lepton:
PLUMED:     (exp((20)/(x)))*((-20)/(square(x)))
PLUMED: Action SUM
PLUMED:   with label dnh_mec_min
PLUMED:   with arguments : 
PLUMED:    vector with label dnh_me_min 
PLUMED: Action CUSTOM
PLUMED:   with label dnh_min
PLUMED:   with arguments : 
PLUMED:    scalar with label dnh_mec_min 
PLUMED:   with function : 20.0/log(x)
PLUMED:   with variables : x
PLUMED:   function as parsed by lepton: (20)/(log(x))
PLUMED:   derivatives as computed by lepton:
PLUMED:     (-20*(recip(x)))/(square(log(x)))
PLUMED:   not calculating when all arguments are zero 
PLUMED: Action CUSTOM
PLUMED:   with label dnh_me_max
PLUMED:   with arguments : 
PLUMED:    vector with label dnh 
PLUMED:   with function : exp(x/0.05)
PLUMED:   with variables : x
PLUMED:   function as parsed by lepton: exp(20*(x))
PLUMED:   derivatives as computed by lepton:
PLUMED:     20*(exp(20*(x)))
PLUMED: Action SUM
PLUMED:   with label dnh_mec_max
PLUMED:   with arguments : 
PLUMED:    vector with label dnh_me_max 
PLUMED: Action CUSTOM
PLUMED:   with label dnh_max
PLUMED:   with arguments : 
PLUMED:    scalar with label dnh_mec_max 
PLUMED:   with function : 0.05*log(x)
PLUMED:   with variables : x
PLUMED:   function as parsed by lepton: 0.05*(log(x))
PLUMED:   derivatives as computed by lepton:
PLUMED:     0.05*(recip(x))
PLUMED: Action COORDINATIONNUMBER
PLUMED:   with label c1
PLUMED: Action GROUP
PLUMED:   with label c1_grp
PLUMED:   list of atoms:
PLUMED:  1001
PLUMED: Action CONTACT_MATRIX
PLUMED:   with label c1_mat
PLUMED: Action CONTACT_MATRIX_PROPER
PLUMED:   with label c1_mat
PLUMED:   atoms in GROUPA 1001 
PLUMED:   atoms in GROUPB 1002 1003 1004 
PLUMED:   Bibliography [3]
PLUMED:   switching function cutoff is 2.  Using rational switching function with parameters d0=0 nn=6 mm=12 
PLUMED:   set link cell cutoff to 13.625841 
PLUMED: Action ONES
PLUMED:   with label c1_ones
PLUMED: Action CONSTANT
PLUMED:   with label c1_ones
PLUMED:   read in 3 values :
PLUMED: Action MATRIX_VECTOR_PRODUCT
PLUMED:   with label c1
PLUMED:   with arguments : 
PLUMED:    matrix with label c1_mat 
PLUMED:    vector with label c1_ones 
PLUMED: Action MEAN
PLUMED:   with label c1_caverage
PLUMED:   with arguments : 
PLUMED:    vector with label c1 
PLUMED: Action CUSTOM
PLUMED:   with label c1_me_min
PLUMED:   with arguments : 
PLUMED:    vector with label c1 
PLUMED:   with function : exp(20.0/x)
PLUMED:   with variables : x
PLUMED:   function as parsed by lepton: exp((20)/(x))
PLUMED:   derivatives as computed by lepton:
PLUMED:     (exp((20)/(x)))*((-20)/(square(x)))
PLUMED: Action SUM
PLUMED:   with label c1_mec_min
PLUMED:   with arguments : 
PLUMED:    vector with label c1_me_min 
PLUMED: Action CUSTOM
PLUMED:   with label c1_min
PLUMED:   with arguments : 
PLUMED:    scalar with label c1_mec_min 
PLUMED:   with function : 20.0/log(x)
PLUMED:   with variables : x
PLUMED:   function as parsed by lepton: (20)/(log(x))
PLUMED:   derivatives as computed by lepton:
PLUMED:     (-20*(recip(x)))/(square(log(x)))
PLUMED:   not calculating when all arguments are zero 
PLUMED: Action CUSTOM
PLUMED:   with label c1_me_max
PLUMED:   with arguments : 
PLUMED:    vector with label c1 
PLUMED:   with function : exp(x/0.05)
PLUMED:   with variables : x
PLUMED:   function as parsed by lepton: exp(20*(x))
PLUMED:   derivatives as computed by lepton:
PLUMED:     20*(exp(20*(x)))
PLUMED: Action SUM
PLUMED:   with label c1_mec_max
PLUMED:   with arguments : 
PLUMED:    vector with label c1_me_max 
PLUMED: Action CUSTOM
PLUMED:   with label c1_max
PLUMED:   with arguments : 
PLUMED:    scalar with label c1_mec_max 
PLUMED:   with function : 0.05*log(x)
PLUMED:   with variables : x
PLUMED:   function as parsed by lepton: 0.05*(log(x))
PLUMED:   derivatives as computed by lepton:
PLUMED:     0.05*(recip(x))
PLUMED: Action COORDINATION
PLUMED:   with label cnh1
PLUMED:   between two groups of 1 and 1 atoms
PLUMED:   first group:
PLUMED:   1001  
PLUMED:   second group:
PLUMED:   1002  
PLUMED:   using periodic boundary conditions
PLUMED:   contacts are counted with cutoff 2.  Using rational switching function with parameters d0=0 nn=6 mm=12
PLUMED: Action COORDINATION
PLUMED:   with label cnh2
PLUMED:   between two groups of 1 and 1 atoms
PLUMED:   first group:
PLUMED:   1001  
PLUMED:   second group:
PLUMED:   1003  
PLUMED:   using periodic boundary conditions
PLUMED:   contacts are counted with cutoff 2.  Using rational switching function with parameters d0=0 nn=6 mm=12
PLUMED: Action COORDINATION
PLUMED:   with label cnh3
PLUMED:   between two groups of 1 and 1 atoms
PLUMED:   first group:
PLUMED:   1001  
PLUMED:   second group:
PLUMED:   1004  
PLUMED:   using periodic boundary conditions
PLUMED:   contacts are counted with cutoff 2.  Using rational switching function with parameters d0=0 nn=6 mm=12
PLUMED: Action CUSTOM
PLUMED:   with label ctot
PLUMED:   with arguments : 
PLUMED:    scalar with label cnh1 
PLUMED:    scalar with label cnh2 
PLUMED:    scalar with label cnh3 
PLUMED:   with function : x+y+z
PLUMED:   with variables : x y z
PLUMED:   function as parsed by lepton: ((x)+(y))+(z)
PLUMED:   derivatives as computed by lepton:
PLUMED:     1
PLUMED:     1
PLUMED:     1
PLUMED:   not calculating when all arguments are zero 
PLUMED: Action UPPER_WALLS
PLUMED:   with label uwall
PLUMED:   with arguments : 
PLUMED:    scalar with label dnh_max 
PLUMED:   added component to this action:  uwall.bias 
PLUMED:   at 6.000000
PLUMED:   with an offset 0.000000
PLUMED:   with force constant 200.000000
PLUMED:   and exponent 2.000000
PLUMED:   rescaled 1.000000
PLUMED:   added component to this action:  uwall.force2 
PLUMED: Action OPES_METAD_EXPLORE
PLUMED:   with label opes1
PLUMED:   with arguments : 
PLUMED:    scalar with label ctot 
PLUMED:   added component to this action:  opes1.bias 
PLUMED: WARNING for action OPES_METAD_EXPLORE with label opes1 : using TEMP=600 while MD engine uses 299.478
PLUMED:  
PLUMED:   added component to this action:  opes1.rct 
PLUMED:   added component to this action:  opes1.zed 
PLUMED:   added component to this action:  opes1.neff 
PLUMED:   added component to this action:  opes1.nker 
PLUMED:   temperature = 600
PLUMED:   beta = 0.200454
PLUMED:   depositing new kernels with PACE = 200
PLUMED:   expected BARRIER is 200
PLUMED:   using target distribution with BIASFACTOR gamma = 40.0908
PLUMED:   adaptive SIGMA will be used, with ADAPTIVE_SIGMA_STRIDE = 2000
PLUMED:     thus the first x kernel depositions will be skipped, x = ADAPTIVE_SIGMA_STRIDE/PACE = 10
PLUMED:   kernels are truncated with KERNELS_CUTOFF = 8.95442
PLUMED:   the value at cutoff is = 3.87965e-18
PLUMED:   regularization EPSILON = 0.358588
PLUMED:   kernels will be compressed when closer than COMPRESSION_THRESHOLD = 1
PLUMED:   Bibliography: [4][5]
PLUMED: Action PRINT
PLUMED:   with label @48
PLUMED:   with stride 50
PLUMED:   with arguments : 
PLUMED:    vector with label dnh 
PLUMED:    vector with label dnh_me_min 
PLUMED:    scalar with label dnh_mec_min 
PLUMED:    scalar with label dnh_min 
PLUMED:    vector with label dnh_me_max 
PLUMED:    scalar with label dnh_mec_max 
PLUMED:    scalar with label dnh_max 
PLUMED:    matrix with label c1_mat 
PLUMED:    vector with label c1_ones 
PLUMED:    vector with label c1 
PLUMED:    scalar with label c1_caverage 
PLUMED:    vector with label c1_me_min 
PLUMED:    scalar with label c1_mec_min 
PLUMED:    scalar with label c1_min 
PLUMED:    vector with label c1_me_max 
PLUMED:    scalar with label c1_mec_max 
PLUMED:    scalar with label c1_max 
PLUMED:    scalar with label cnh1 
PLUMED:    scalar with label cnh2 
PLUMED:    scalar with label cnh3 
PLUMED:    scalar with label ctot 
PLUMED:    scalar with label uwall.bias 
PLUMED:    scalar with label uwall.force2 
PLUMED:    scalar with label opes1.bias 
PLUMED:    scalar with label opes1.rct 
PLUMED:    scalar with label opes1.zed 
PLUMED:    scalar with label opes1.neff 
PLUMED:    scalar with label opes1.nker 
PLUMED:   on file COLVAR
PLUMED:   with format  %f
PLUMED: Action FLUSH
PLUMED:   with label @49
PLUMED:   with stride 1
PLUMED: END FILE: plumed.dat
PLUMED: Timestep: 1000.000000
PLUMED: KbT: 2.490000
PLUMED: Relevant bibliography:
PLUMED:   [1] The PLUMED consortium, Nat. Methods 16, 670 (2019)
PLUMED:   [2] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)
PLUMED:   [3] Tribello, Giberti, Sosso, Salvalaglio and Parrinello, J. Chem. Theory Comput. 13, 1317 (2017)
PLUMED:   [4] M. Invernizzi and M. Parrinello, J. Phys. Chem. Lett. 11, 2731-2736 (2020)
PLUMED:   [5] M. Invernizzi and M. Parrinello, J. Chem. Theory Comput. 18, 3988-3996 (2022)
PLUMED: Please read and cite where appropriate!
PLUMED: Finished setup
PLUMED:                                               Cycles        Total      Average      Minimum      Maximum
PLUMED:                                                    1     0.011648     0.011648     0.011648     0.011648
