PLUMED: PLUMED is starting
PLUMED: Version: 2.10.0 (git: 09264719e) compiled on Jun 10 2026 at 10:34:57
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: logn_jeff.dat
PLUMED: Action GROUP
PLUMED:   with label batoms
PLUMED:   importing group 'batoms' from index file index.ndx
PLUMED:   list of atoms:
PLUMED:  472 499 510 527 537 558 579 589 608 619 640 651 661 680 699 718 728 747 763 781 790 802 811 830 846
PLUMED:  857 874 884 900 919 941 956 980 990 1009 1026 1040 1054 1068 1082 1103 1122 1138 1154 1165 1184 1194 1210 1220 1232
PLUMED:  1251 1270 1286 1296 1310 1329 1345 1365 1376 1400 1416 1432 1453 1472 1487 1503 1515 1522 1531 1547 1571 1585 1616 1640 1659
PLUMED:  1670 1680 1692 1708 1728 1744 1758 1777 1789 1805 1822 1839 1850 1864 1874 1885 1904 1928 1942 1961 1972 1982 2001 2012 2031
PLUMED:  2043 2067 2088 2102 2112 2128 2144 2164 2175 2191 2208 2229 2246 2261 2270 2282 2291 2308 2319 2330 2341 2365 2389 2405 2415
PLUMED:  2434 2451 2470 2484 2494 2510 2534 2550 2569 2579 2609 2625 2636 2650 2661 2680 2699 2726 2746 2760 2774 2786 2795 2810 2821
PLUMED:  2835 2851 2861 2872 2891 2902 2919 2930 2942 2962 2978 2997 3018 3029 3040 3056 3072 3083 3103 3124 3146 3157 3175 3184 3200
PLUMED:  3214 3230 3249 3265 3296 3320 3339 3360 3376 3392 3411 3433 3450 3474 3498 3522 3544 3558 3577 3597 3612 3629 3648 3672 3691
PLUMED:  3703 3716 3725 3744 3768 3787 3809 3828 3849 3871 3897 3910 3919 3940 3961 3975 3992 4001 4018 4027 4044 4063 4082 4096 4118
PLUMED:  4132 4143 4154 4173 4187 4197 4207 4229 4240 4255 4274 4286 4308 4318 4344 4368 4382 4396 4408 4417 4433 4452 4466 4488 4500
PLUMED:  4515 4525 4540 4562 4581 4601 4615 4632 4644 4660 4672 4682 4692 4708 4730 4739 4758 4777 4801 4825 4847 4866 4891 4902 4918
PLUMED:  4939 4951 4962 4981 4993 5003 5019 5043 5067 5077 5087 5106 5125 5139 5156 5172 5192 5209 5224 5233 5260 5269 5285 5293 5302
PLUMED:  5322 5336 5350 5361 5380 5404 5421 5440 5457 5474 5496 5520 5544 5556 5571 5581 5591 5607 5621 5640 5650 5672 5683 5707 5731
PLUMED:  5752 5766 5783 5800 5811 5825 5849 5859 5881 5905 5921 5940 5954 5968 5988 6012 6024 6033 6047 6071 6083 6093 6112 6121 6140
PLUMED:  6151 6170 6194 6209 6231 6253 6263 6277 6294 6311 6327 6337 6356 6372 6398 6408 6428 6463 6474 6498 6520 6531 6551 6571 6590
PLUMED:  6604 6621 6637 6656 6670 6684 6701 6742 6769 6785 6799 6810 6825 6844 6865 6876 6886 6900 6914 6938 6955 6964 6985 7001 7015
PLUMED:  7026 7036 7055 7072 7083 7099 7118 7139 7153 7167 7187 7201 7220 7235 7255 7279 7301 7311 7331 7350 7372 7391 7410 7421 7439
PLUMED:  7477 7496 7511 7546 7566 8051 8078 8089 8106 8116 8137 8158 8168 8187 8198 8219 8230 8240 8259 8278 8297 8307 8326 8342 8360
PLUMED:  8369 8381 8390 8409 8425 8436 8453 8463 8479 8498 8520 8535 8559 8569 8588 8605 8619 8633 8647 8661 8682 8701 8717 8733 8744
PLUMED:  8763 8773 8789 8799 8811 8830 8849 8865 8875 8889 8908 8924 8944 8955 8979 8995 9011 9032 9051 9066 9082 9094 9101 9110 9126
PLUMED:  9150 9164 9195 9219 9238 9249 9259 9271 9287 9307 9323 9337 9356 9368 9384 9401 9418 9429 9443 9453 9464 9483 9507 9521 9540
PLUMED:  9551 9561 9580 9591 9610 9622 9646 9667 9681 9691 9707 9723 9743 9754 9770 9787 9808 9825 9840 9849 9861 9870 9887 9898 9909
PLUMED:  9920 9944 9968 9984 9994 10013 10030 10049 10063 10073 10089 10113 10129 10148 10158 10188 10204 10215 10229 10240 10259 10278 10305 10325 10339
PLUMED:  10353 10374 10389 10400 10414 10430 10440 10451 10470 10481 10498 10509 10521 10541 10557 10576 10597 10608 10619 10635 10651 10662 10682 10703 10725
PLUMED:  10736 10754 10763 10779 10793 10809 10828 10844 10875 10899 10918 10939 10955 10971 10990 11012 11029 11053 11077 11101 11123 11137 11156 11176 11191
PLUMED:  11208 11227 11251 11270 11282 11295 11304 11323 11347 11366 11388 11407 11428 11450 11476 11489 11498 11519 11540 11554 11571 11580 11597 11606 11623
PLUMED:  11642 11661 11675 11697 11711 11722 11733 11752 11766 11776 11786 11808 11819 11834 11853 11865 11887 11897 11923 11947 11961 11975 11987 11996 12012
PLUMED:  12031 12045 12067 12079 12094 12104 12119 12141 12160 12180 12194 12211 12223 12239 12251 12261 12271 12287 12309 12318 12337 12356 12380 12404 12426
PLUMED:  12445 12470 12481 12497 12518 12530 12541 12560 12572 12582 12598 12622 12646 12656 12666 12685 12704 12718 12735 12751 12771 12788 12803 12812 12839
PLUMED:  12848 12864 12872 12881 12901 12915 12929 12940 12959 12983 13000 13019 13036 13053 13075 13099 13123 13135 13150 13160 13170 13186 13200 13219 13229
PLUMED:  13251 13262 13286 13310 13331 13345 13362 13379 13390 13404 13428 13438 13460 13484 13500 13519 13533 13547 13567 13591 13603 13612 13626 13650 13662
PLUMED:  13672 13691 13700 13719 13730 13749 13773 13788 13810 13832 13842 13856 13873 13890 13906 13916 13935 13951 13977 13987 14007 14042 14053 14077 14099
PLUMED:  14110 14130 14150 14169 14183 14200 14216 14235 14249 14263 14280 14321 14348 14364 14378 14389 14404 14423 14444 14455 14465 14479 14493 14517 14534
PLUMED:  14543 14564 14580 14594 14605 14615 14634 14651 14662 14678 14697 14718 14732 14746 14766 14780 14799 14814 14834 14858 14880 14890 14910 14929 14951
PLUMED:  14970 14989 15000 15018 15056 15075 15090 15125 15145
PLUMED: Action BAIES
PLUMED:   with label baies
PLUMED:   number of atoms involved : 859
PLUMED:   AF2 fit parameters file : logn.out
PLUMED:   prior type : JEFFREYS
PLUMED:   noise model type : lognormal
PLUMED:   number of pairs involved : 2507
PLUMED:   temperature of the system in energy unit : 2.478541
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     0.016903     0.016903     0.016903     0.016903
