PLUMED: PLUMED is starting
PLUMED: Version: 2.11.0-dev (git: b9f2f564f) compiled on Jun 10 2026 at 10:43:37
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_master
PLUMED: LibraryPath: /home/runner/opt/lib/libplumed_masterKernel.so
PLUMED: For installed feature, see /home/runner/opt/lib/plumed_master/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: logn_jeff.dat
PLUMED: Action GROUP
PLUMED:   with label batoms
PLUMED:   importing group 'batoms' from index file index.ndx
PLUMED:   list of atoms:
PLUMED:  319 357 381 412 434 456 473 482 506 525 540 560 579 591 603 614 631 651 659 668 690 704 714 729 748
PLUMED:  767 791 815 834 851 875 894 909 930 952 968 990 1011 1030 1046 1066 1091 1102 1124 1143 1155 1169 1204 1223 1247
PLUMED:  1261 1280 1308 1353 1367 1378 1400 1411 1422 1438 1453 1469 1484 1495 1508 1519 1534 1553 1572 1586 1607 1626 1643 1654 1668
PLUMED:  1679 1699 1713 1725 1740 1754 1776 1792 1809 1818 1837 1849 1864 1880 1897 1917 1937 1949 1961 1985 2004 2015 2030 2046 2056
PLUMED:  2070 2089 2108 2118 2133 2145 2154 2174 2190 2206 2225 2244 2253 2262 2281 2293 2315 2329 2349 2369 2378 2396 2407 2425 2437
PLUMED:  2448 2467 2477 2499 2518 2538 2552 2573 2583 2595 2617 2636 2650 2672 2691 2705 2715 2734 2745 2759 2774 2783 2792 2802 2817
PLUMED:  2827 2841 2858 2869 2888 2912 2934 2972 2994 3011 3021 3033 3054 3068 3080 3092 3111 3127 3149 3166 3175 3186 3203 3218 3238
PLUMED:  3259 3270 3280 3296 3307 3331 3348 3365 3382 3404 3423 3434 3448 3475 3486 3507 3526 3540 3551 3565 3576 3591 3606 3626 3645
PLUMED:  3667 3687 3707 3729 3743 3765 3787 3811 3825 3847 3861 4247 4257 4288 4310 4332 4349 4358 4382 4401 4416 4436 4455 4467 4479
PLUMED:  4490 4507 4527 4535 4544 4566 4580 4590 4605 4624 4643 4667 4691 4710 4727 4751 4770 4785 4806 4828 4844 4866 4887 4906 4922
PLUMED:  4942 4967 4978 5000 5019 5031 5045 5080 5099 5123 5137 5156 5184 5229 5243 5254 5276 5287 5298 5314 5329 5345 5360 5371 5384
PLUMED:  5395 5410 5429 5448 5462 5483 5502 5519 5530 5544 5555 5575 5589 5601 5616 5630 5652 5668 5685 5694 5713 5725 5740 5756 5773
PLUMED:  5793 5813 5825 5837 5861 5880 5891 5906 5922 5932 5946 5965 5984 5994 6009 6021 6030 6050 6066 6082 6101 6120 6129 6138 6157
PLUMED:  6169 6191 6205 6225 6245 6254 6272 6283 6301 6313 6324 6343 6353 6375 6394 6414 6428 6449 6459 6471 6493 6512 6526 6548 6567
PLUMED:  6581 6591 6610 6621 6635 6650 6659 6668 6678 6693 6703 6717 6734 6745 6764 6788 6810 6848 6870 6887 6897 6909 6930 6944 6956
PLUMED:  6968 6987 7003 7025 7042 7051 7062 7079 7094 7114 7135 7146 7156 7172 7183 7207 7224 7241 7258 7280 7299 7310 7324 7351 7362
PLUMED:  7383 7402 7416 7427 7441 7452 7467 7482 7502 7521 7543 7563 7583 7605 7619 7641 7663 7687 7701 7723 7737 8071 8109 8133 8164
PLUMED:  8186 8208 8225 8234 8258 8277 8292 8312 8331 8343 8355 8366 8383 8403 8411 8420 8442 8456 8466 8481 8500 8519 8543 8567 8586
PLUMED:  8603 8627 8646 8661 8682 8704 8720 8742 8763 8782 8798 8818 8843 8854 8876 8895 8907 8921 8956 8975 8999 9013 9032 9060 9105
PLUMED:  9119 9130 9152 9163 9174 9190 9205 9221 9236 9247 9260 9271 9286 9305 9324 9338 9359 9378 9395 9406 9420 9431 9451 9465 9477
PLUMED:  9492 9506 9528 9544 9561 9570 9589 9601 9616 9632 9649 9669 9689 9701 9713 9737 9756 9767 9782 9798 9808 9822 9841 9860 9870
PLUMED:  9885 9897 9906 9926 9942 9958 9977 9996 10005 10014 10033 10045 10067 10081 10101 10121 10130 10148 10159 10177 10189 10200 10219 10229 10251
PLUMED:  10270 10290 10304 10325 10335 10347 10369 10388 10402 10424 10443 10457 10467 10486 10497 10511 10526 10535 10544 10554 10569 10579 10593 10610 10621
PLUMED:  10640 10664 10686 10724 10746 10763 10773 10785 10806 10820 10832 10844 10863 10879 10901 10918 10927 10938 10955 10970 10990 11011 11022 11032 11048
PLUMED:  11059 11083 11100 11117 11134 11156 11175 11186 11200 11227 11238 11259 11278 11292 11303 11317 11328 11343 11358 11378 11397 11419 11439 11459 11481
PLUMED:  11495 11517 11539 11563 11577 11599 11613 11999 12040 12062 12084 12101 12110 12134 12153 12168 12188 12207 12219 12231 12242 12259 12279 12287 12296
PLUMED:  12318 12332 12342 12357 12376 12395 12419 12443 12462 12479 12503 12522 12537 12558 12580 12596 12618 12639 12658 12674 12694 12719 12730 12752 12771
PLUMED:  12783 12797 12832 12851 12875 12889 12908 12936 12981 12995 13006 13028 13039 13050 13066 13081 13097 13112 13123 13136 13147 13162 13181 13200 13214
PLUMED:  13235 13254 13271 13282 13296 13307 13327 13341 13353 13368 13382 13404 13420 13437 13446 13465 13477 13492 13508 13525 13545 13565 13577 13589 13613
PLUMED:  13632 13643 13658 13674 13684 13698 13717 13736 13746 13761 13773 13782 13802 13818 13834 13853 13872 13881 13890 13909 13921 13943 13957 13977 13997
PLUMED:  14006 14024 14035 14053 14065 14076 14095 14105 14127 14146 14166 14180 14201 14211 14223 14245 14264 14278 14300 14319 14333 14343 14362 14373 14387
PLUMED:  14402 14411 14420 14430 14445 14455 14469 14486 14497 14516 14540 14562 14600 14622 14639 14649 14661 14682 14696 14708 14720 14739 14755 14777 14794
PLUMED:  14803 14814 14831 14846 14866 14887 14898 14908 14924 14935 14959 14976 14993 15010 15032 15051 15062 15076 15103 15114 15135 15154 15168 15179 15193
PLUMED:  15204 15219 15234 15254 15273 15295 15315 15335 15357 15371 15393 15415 15439 15453 15475 15489
PLUMED: Action BAIES
PLUMED:   with label baies
PLUMED:   number of atoms involved : 841
PLUMED:   AF2 fit parameters file : logn.out
PLUMED:   prior type : JEFFREYS
PLUMED:   noise model type : lognormal
PLUMED:   number of pairs involved : 3069
PLUMED:   temperature of the system in energy unit : 0.020608
PLUMED:   minimum value of sigma : -1.000000
PLUMED:   using periodic boundary conditions
PLUMED:   added component to this action: baies.ene 
PLUMED:   Bibliography [3][4]
PLUMED: Action PRINT
PLUMED:   with label @2
PLUMED:   with stride 500
PLUMED:   with arguments : 
PLUMED:    scalar with label baies.ene 
PLUMED:   on file COLVAR
PLUMED:   with format  %f
PLUMED: Action BIASVALUE
PLUMED:   with label bbias
PLUMED:   with arguments : 
PLUMED:    scalar with label baies.ene 
PLUMED:   added component to this action: bbias.bias 
PLUMED:   multiple time step 4 [5]
PLUMED:   added component to this action: bbias.baies.ene_bias 
PLUMED: END FILE: logn_jeff.dat
PLUMED: Timestep: 1.000000
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] Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)
PLUMED:   [4] Schnapka, Morozova, Sen, Bonomi, bioRxiv (2025) doi: XXX
PLUMED:   [5] Ferrarotti, Bottaro, Perez-Villa, and Bussi, J. Chem. Theory Comput. 11, 139 (2015)
PLUMED: Please read and cite where appropriate!
PLUMED: Finished setup
PLUMED:                                               Cycles        Total      Average      Minimum      Maximum
PLUMED:                                                    1     0.019423     0.019423     0.019423     0.019423
