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:  7 22 31 48 65 82 99 116 133 148 162 181 202 222 237 246 263 285 307 322 344 360 375 392 411
PLUMED:  430 440 455 475 492 511 528 543 558 570 589 611 633 649 666 690 714 731 748 770 785 802 814 836 845
PLUMED:  864 888 907 922 936 953 968 983 993 1004 1020 1042 1059 1081 1092 1106 1127 1143 1167 1178 1195 1206 1219 1228 1239
PLUMED:  1254 1268 1277 1289 1309 1328 1339 1358 1370 1387 1394 1403 1417 1431 1451 1475 1491 1508 1527 1543 1565 1579 1588 1601 1638
PLUMED:  1647 1664 1688 1699 1715 1737 1751 1773 1790 1807 1824 1845 1856 1878 1889 1904 1916 1926 1943 1955 1964 1978 1988 2003 2020
PLUMED:  2039 2059 2071 2092 2111 2122 2137 2148 2167 2178 2190 2210 2229 2241 2263 2280 2297 2314 2336 2353 2375 2397 2419 2430 2447
PLUMED:  2456 2476 2490 2510 2521 2544 2555 2571 2595 2612 2627 2639 2658 2670 2690 2699 2718 2737 2756 2770 2794 2808 2828 2837 2857
PLUMED:  2879 2889 2898 2907 2917 2930 2939 2953 2967 2983 2997 3006 3025 3044 3068 3080 3090 3109 3131 3155 3186 3198 3218 3233 3250
PLUMED:  3262 3278 3294 3304 3321 3337 3351 3363 3377 3393 3403 3417 3434 3453 3464 3475 3496 3517 3532 3544 3561 3578 3589 3604 3618
PLUMED:  3627 3644 3663 3677 3686 3698 3707 3718 3732 3742 3753 3774 3791 3806 3821 3838 3855 3869 3885 3900 3919 3948 3957 3969 3982
PLUMED:  3991 4015 4032 4043 4059 4073 4087 4102 4124 4133 4143 4161 4170 4182 4200 4215 4234 4246 4261 4281 4300 4319 4334 4355 4367
PLUMED:  4391 4410 4426 4438 4453 4464 4485 4502 4511 4520 4537 4554 4573 4594 4609 4631 4650 4667 4674 4683 4705 4726 4741 4750 4765
PLUMED:  4784 4800 4824 4843 4859 4878 4897 4921 4940 4956 4968 4983 4997 5016 5035 5055 5070 5079 5094 5104 5115 5130 5147 5166 5190
PLUMED:  5204 5226 5235 5245 5265 5280 5294 5318 5338 5354 5365 5382 5398 5413 5424 5436 5457 5469 5493 5515 5532 5551 5572 5586 5605
PLUMED:  5624 5635 5649 5666 5675 5694 5721 5732 5743 5757 5771 5783 5794 5806 5825 5841 5865 5889 5899 5910 5925 5936 5952 5963 5977
PLUMED:  6001 6011 6021 6038 6055 6066 6077 6085 6094 6113 6121 6130 6146 6165 6179 6203 6220 6244 6259 6270 6294 6305 6320 6332 6348
PLUMED:  6365 6389 6408 6422 6436 6445 6461 6471 6480 6491 6507 6528 6550 6569 6589 6600 6611 6631 6653 6668 6692 6712 6729 6739 6750
PLUMED:  6766 6790 6814 6833 6850 6861 6872 6883 6898 6917 6931 6951 6970 6985 6996 7011 7024 7033 7042 7051 7073 7082 7092 7102 7121
PLUMED:  7137 7148 7158 7174 7184 7195 7217 7249 7260 7277 7303
PLUMED: Action BAIES
PLUMED:   with label baies
PLUMED:   number of atoms involved : 461
PLUMED:   AF2 fit parameters file : logn.out
PLUMED:   prior type : JEFFREYS
PLUMED:   noise model type : lognormal
PLUMED:   number of pairs involved : 1627
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     0.013332     0.013332     0.013332     0.013332
