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:  168 189 209 224 233 247 266 286 301 318 337 361 380 392 405 414 433 457 476 498 517 538 560 572 586
PLUMED:  599 608 629 650 664 681 690 707 716 733 752 771 785 807 821 832 843 862 876 886 896 918 929 944 963
PLUMED:  975 997 1007 1033 1057 1071 1085 1097 1106 1122 1141 1155 1177 1189 1204 1214 1229 1251 1270 1290 1304 1321 1333 1349 1361
PLUMED:  1371 1381 1397 1419 1428 1447 1466 1490 1514 1536 1555 1580 1591 1607 1628 1640 1651 1670 1692 1708 1732 1756 1766 1776 1795
PLUMED:  1814 1828 1845 1861 1881 1898 1913 1922 1949 1958 1974 1982 1991 2011 2025 2039 2050 2069 2093 2110 2129 2146 2163 2185 2209
PLUMED:  2233 2245 2260 2270 2280 2296 2310 2329 2339 2361 2372 2396 2420 2441 2455 2472 2489 2500 2514 2538 2548 2570 2594 2610 2629
PLUMED:  2643 2657 2677 2701 2713 2722 2736 2760 2772 2782 2803 2813 2823 2835 2866 2890 2906 2929 2944 2953 2972 2988 3005 3016 3035
PLUMED:  3054 3070 3089 3099 3118 3134 3152 3161 3175 3191 3210 3226 3245 3259 3269 3288 3298 3320 3355 3379 3398 3415 3429 3445 3459
PLUMED:  3473 3494 3514 3533 3547 3558 3577 3587 3598 3608 3620 3639 3655 3670 3679 3698 3708 3724 3743 3754 3772 3781 3791 3801 3818
PLUMED:  3837 3856 3870 3892 3906 3930 3944 3962 3971 3985 4005 4029 4039 4054 4074 4098 4112 4123 4142 4154 4170 4189 4200 4216 4230
PLUMED:  4240 4251 4270 4285 4299 4318 4329 4345 4364 4374 4390 4402 4426 4447 4467 4477 4496 4510 4524 4535 4555 4577 4598 4615 4626
PLUMED:  4645 4664 4678 4700 4714 4736 4746 4770 4786 4805 4824 4843 4860 4876 4900 4919 4935 4944 4953 4972 4986 4997 5017 5039 5050
PLUMED:  5069 5086 5103 5120 5144 5165 5189 5199 5213 5230 5247 5262 5272 5291 5305 5315 5336 5346 5361 5376 5390 5400 5410 5422 5442
PLUMED:  5462 5476 5490 5507 5517 5538 5548 5577 5588 5599 5618 5634 5645 5665 5686 5705 5716 5735 5751 5770 5787 5803 5823 5839 5860
PLUMED:  5871 5895 5911 5931 5948 5963 5973 5995 6019 6036 6055 6072 6094 6125 6147 6167 6177 6196 6218 6233 6250 6272 6282 6301 6323
PLUMED:  6337 6354 6363 6382 6401 6416 6425 6439 6459 6473 6492 6503 6527 6549 6560 6580 6600 6619 6635 6649 6668 6684 6701 6717 6736
PLUMED:  6753 6765 6779 6798 6817 6841 6863 6878 6894 6915 6934 6953 6972 6986 7010 7027 7036 7057 7073 7087 7096 7105 7125 7142 7153
PLUMED:  7172 7191 7212 7223 7247 7261 7272 7284 7304 7328 7347 7357 7377 7394 7409 7428 7458 7477 7501 7525 7591 7608 7624 7641 7660
PLUMED:  7677 7692 7701 7708 7715 7724 7743 7759 7776 7784 7791 7800 7811 7830 7854 7873 7884 7894 7904 7914 7923 7932 7943 7962 7982
PLUMED:  7992 8011 8025 8044 8059 8068 8092 8113 8137 8154 8185 8207 8224 8248 8263 8282 8298 8308 8318 8337 8354 8363 8370 8379 8393
PLUMED:  8407 8421 8442 8466 8477 8493 8513 8522 8546 8566 8580 8599 8610 8634 8646 8660 8670 8680 8694 8708 8724 8745 8764 8781 8798
PLUMED:  8812 8823 8842 8867 8878 8893 8905 8919 8929 8945 8966 8987 8997 9011 9027 9049 9061 9079 9088 9098 9117 9136 9157 9169 9190
PLUMED:  9202 9223 9245 9254 9269 9278 9292 9309 9325 9339 9355 9366
PLUMED: Action BAIES
PLUMED:   with label baies
PLUMED:   number of atoms involved : 562
PLUMED:   AF2 fit parameters file : logn.out
PLUMED:   prior type : JEFFREYS
PLUMED:   noise model type : lognormal
PLUMED:   number of pairs involved : 1765
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     0.013588     0.013588     0.013588     0.013588
