Amber12 Module: addles set up Locally Enhanced Sampling topology add_les> ~ add_les> ~ all file names are specified at the beginning, before "action" add_les> ~ add_les> ~ file to read prmtop add_les> ~ add_les> file rprm name=(prmtop) read The following unit number was assigned 26 | New format PARM file being parsed. | Version = 1.000 Date = 02/04/04 Time = 14:12:56 Checking topology sizes against compiled limits Checking topology sizes against compiled limits add_les> ~ add_les> ~ file to read coordinates, velocities and box (this is a restart add_les> file) add_les> ~ add_les> file rcvb name=(md.solv.crd) read The following unit number was assigned 27 Coords, velocities and box from unit 27 Reading coordinates from input file Reading velocities from input file Reading box coords from input file add_les> ~ add_les> ~ file to write prmtop add_les> ~ add_les> file wprm name=(LES.prmtop) wovr The following unit number was assigned 28 add_les> ~ add_les> ~ file to write coordinates (and velocities and box since they were add_les> read in) add_les> ~ add_les> file wcrd name=(LES.crd) wovr The following unit number was assigned 29 add_les> ~ add_les> ~ now the action command reads the files and tells addles to process add_les> commands add_les> ~ add_les> action add_les> ~ add_les> ~ do not scale masses of copied particles add_les> ~ add_les> omas All masses will be left at initial values add_les> ~ add_les> ~ divide the peptide into 2 regions. add_les> ~ use the CCA option to place the division between carbonyl and alpha add_les> carbon add_les> ~ use the "or" to make sure all atoms in the terminal residues add_les> ~ are included since the CCA option places the region division at C/CA add_les> ~ and we want all of the terminal residue included on each end add_les> ~ add_les> ~ make 5 copies of first half and only 4 of second half- normally add_les> ~ the same number of copies is used, this is just for illustrating how add_les> ~ this can be done and to make a more rigorous test add_les> ~ add_les> ~ "spac" defines a LES subspace (or region) add_les> ~ Modifying velocities, factor is 1.06308 Modifying velocities, factor is 0.96491 Modifying velocities, factor is 0.94255 Modifying velocities, factor is 1.04109 Modifying velocities, factor is 1.04265 Modifying velocities, factor is 0.95074 Modifying velocities, factor is 0.96263 Modifying velocities, factor is 0.93288 Modifying velocities, factor is 1.02177 Modifying velocities, factor is 1.03218 Modifying velocities, factor is 1.06513 Modifying velocities, factor is 0.90060 Modifying velocities, factor is 0.96068 Modifying velocities, factor is 1.02132 Modifying velocities, factor is 0.94695 Modifying velocities, factor is 1.05317 Modifying velocities, factor is 1.05265 Modifying velocities, factor is 1.04876 Modifying velocities, factor is 0.93265 Modifying velocities, factor is 0.93046 Modifying velocities, factor is 1.04496 Modifying velocities, factor is 1.04714 Modifying velocities, factor is 0.97130 Modifying velocities, factor is 1.00325 Modifying velocities, factor is 1.07816 Modifying velocities, factor is 1.03900 Modifying velocities, factor is 0.99781 Modifying velocities, factor is 0.90456 Modifying velocities, factor is 0.99441 Modifying velocities, factor is 0.99276 Modifying velocities, factor is 0.90543 Modifying velocities, factor is 0.92795 Modifying velocities, factor is 0.91805 Modifying velocities, factor is 0.97787 Modifying velocities, factor is 0.97592 Modifying velocities, factor is 1.03060 Modifying velocities, factor is 0.97128 Modifying velocities, factor is 1.04970 Modifying velocities, factor is 0.93065 Modifying velocities, factor is 0.96615 Modifying velocities, factor is 1.03250 Modifying velocities, factor is 1.03110 Modifying velocities, factor is 0.99198 Modifying velocities, factor is 0.96525 Modifying velocities, factor is 0.96212 Modifying velocities, factor is 1.02314 Modifying velocities, factor is 0.95389 Modifying velocities, factor is 0.95843 Modifying velocities, factor is 0.92278 Modifying velocities, factor is 0.94101 Modifying velocities, factor is 1.01391 Modifying velocities, factor is 0.97412 Modifying velocities, factor is 1.05880 Modifying velocities, factor is 0.90015 Modifying velocities, factor is 1.04883 Modifying velocities, factor is 1.06651 Modifying velocities, factor is 0.97473 Modifying velocities, factor is 1.05110 Modifying velocities, factor is 0.95922 Modifying velocities, factor is 1.06521 Modifying velocities, factor is 0.94316 Modifying velocities, factor is 0.93107 Modifying velocities, factor is 0.92606 Modifying velocities, factor is 0.91493 Modifying velocities, factor is 1.05818 Modifying velocities, factor is 0.98493 Modifying velocities, factor is 1.08831 Modifying velocities, factor is 0.96420 Modifying velocities, factor is 1.07861 Modifying velocities, factor is 0.93541 Modifying velocities, factor is 1.02322 Modifying velocities, factor is 1.02146 Modifying velocities, factor is 0.98451 Modifying velocities, factor is 0.93823 Modifying velocities, factor is 1.04297 Modifying velocities, factor is 0.91374 Modifying velocities, factor is 0.93629 Modifying velocities, factor is 1.03731 Modifying velocities, factor is 0.99237 Modifying velocities, factor is 1.08533 Modifying velocities, factor is 1.05536 Modifying velocities, factor is 1.00487 Modifying velocities, factor is 1.00875 Modifying velocities, factor is 1.00466 Modifying velocities, factor is 0.99430 Modifying velocities, factor is 1.02078 Modifying velocities, factor is 1.00272 Modifying velocities, factor is 0.92443 Modifying velocities, factor is 1.03227 Modifying velocities, factor is 0.99045 Modifying velocities, factor is 0.93805 Modifying velocities, factor is 0.92550 Modifying velocities, factor is 0.96325 Modifying velocities, factor is 1.09662 Modifying velocities, factor is 1.03204 Modifying velocities, factor is 1.07714 Modifying velocities, factor is 1.02588 Modifying velocities, factor is 1.08253 Modifying velocities, factor is 0.94886 Modifying velocities, factor is 0.91436 Modifying velocities, factor is 1.02826 Modifying velocities, factor is 1.00666 Modifying velocities, factor is 0.94920 Modifying velocities, factor is 0.96453 Modifying velocities, factor is 1.02778 Modifying velocities, factor is 1.04487 Modifying velocities, factor is 0.99280 Modifying velocities, factor is 1.01225 Modifying velocities, factor is 1.06821 Modifying velocities, factor is 0.99698 Modifying velocities, factor is 1.04786 Modifying velocities, factor is 0.90966 Modifying velocities, factor is 1.01418 Modifying velocities, factor is 0.93487 Modifying velocities, factor is 1.07272 Modifying velocities, factor is 1.04397 Modifying velocities, factor is 0.93712 Modifying velocities, factor is 0.95323 Modifying velocities, factor is 1.02016 Modifying velocities, factor is 1.05364 Modifying velocities, factor is 1.05513 Modifying velocities, factor is 0.91344 Modifying velocities, factor is 1.00734 Modifying velocities, factor is 0.90980 Modifying velocities, factor is 0.92036 Modifying velocities, factor is 1.06370 Modifying velocities, factor is 1.01993 Modifying velocities, factor is 1.08842 Modifying velocities, factor is 0.95709 Modifying velocities, factor is 1.08969 Modifying velocities, factor is 0.98410 Modifying velocities, factor is 1.00708 Modifying velocities, factor is 0.98750 Modifying velocities, factor is 0.90553 Modifying velocities, factor is 1.09680 Modifying velocities, factor is 0.92646 Modifying velocities, factor is 1.03788 Modifying velocities, factor is 0.93222 Modifying velocities, factor is 1.00497 Modifying velocities, factor is 0.90917 Modifying velocities, factor is 0.95424 Modifying velocities, factor is 0.98639 Modifying velocities, factor is 1.00989 Modifying velocities, factor is 0.98101 Modifying velocities, factor is 1.01499 Modifying velocities, factor is 0.96607 Modifying velocities, factor is 0.95486 Modifying velocities, factor is 0.98116 Modifying velocities, factor is 1.06136 Modifying velocities, factor is 0.94414 Modifying velocities, factor is 1.06063 Modifying velocities, factor is 1.03362 Modifying velocities, factor is 0.90906 Modifying velocities, factor is 0.90704 Modifying velocities, factor is 1.01635 Modifying velocities, factor is 0.92182 Modifying velocities, factor is 1.01660 Modifying velocities, factor is 0.97524 Modifying velocities, factor is 0.91105 Modifying velocities, factor is 1.04106 there were 1350 particles; currently 1470 particles there were 1316 nbonh bonds, now there are 1382 there were 34 nbona bonds, now there are 88 there were 0 nbper bonds, now there are 0 there were 85 ntheth angles, now there are 229 there were 47 ntheta angles, now there are 125 there were 0 ngper angles, now there are 0 there were 137 nphih torsions, now there are 368 there were 90 nphia torsions, now there are 237 there were 0 ndper torsions, now there are 0 processing exclusion list finished creating LES subspace Checking topology sizes against compiled limits add_les> ~ Modifying velocities, factor is 1.05269 Modifying velocities, factor is 1.01851 Modifying velocities, factor is 0.90390 Modifying velocities, factor is 1.00412 Modifying velocities, factor is 0.94828 Modifying velocities, factor is 0.97351 Modifying velocities, factor is 1.00353 Modifying velocities, factor is 0.99132 Modifying velocities, factor is 1.05115 Modifying velocities, factor is 0.99403 Modifying velocities, factor is 0.94464 Modifying velocities, factor is 1.06788 Modifying velocities, factor is 0.92570 Modifying velocities, factor is 0.99443 Modifying velocities, factor is 0.95454 Modifying velocities, factor is 0.97735 Modifying velocities, factor is 0.99043 Modifying velocities, factor is 1.01773 Modifying velocities, factor is 0.90741 Modifying velocities, factor is 1.01375 Modifying velocities, factor is 1.07461 Modifying velocities, factor is 1.07529 Modifying velocities, factor is 0.91024 Modifying velocities, factor is 1.06694 Modifying velocities, factor is 0.90690 Modifying velocities, factor is 1.03055 Modifying velocities, factor is 1.08200 Modifying velocities, factor is 1.01153 Modifying velocities, factor is 0.98476 Modifying velocities, factor is 1.01898 Modifying velocities, factor is 1.08496 Modifying velocities, factor is 0.97581 Modifying velocities, factor is 0.98215 Modifying velocities, factor is 1.01051 Modifying velocities, factor is 0.99258 Modifying velocities, factor is 1.06477 Modifying velocities, factor is 1.02129 Modifying velocities, factor is 1.08228 Modifying velocities, factor is 0.92669 Modifying velocities, factor is 0.93045 Modifying velocities, factor is 1.04925 Modifying velocities, factor is 0.94391 Modifying velocities, factor is 0.90937 Modifying velocities, factor is 0.99793 Modifying velocities, factor is 0.98539 Modifying velocities, factor is 1.07479 Modifying velocities, factor is 1.02607 Modifying velocities, factor is 1.00808 Modifying velocities, factor is 0.93832 Modifying velocities, factor is 0.92100 Modifying velocities, factor is 0.90565 Modifying velocities, factor is 1.04506 Modifying velocities, factor is 1.00122 Modifying velocities, factor is 0.92475 Modifying velocities, factor is 1.03143 Modifying velocities, factor is 0.95466 Modifying velocities, factor is 0.92268 Modifying velocities, factor is 0.97546 Modifying velocities, factor is 1.00137 Modifying velocities, factor is 0.93507 Modifying velocities, factor is 0.99924 Modifying velocities, factor is 0.92782 Modifying velocities, factor is 0.92819 Modifying velocities, factor is 0.90968 Modifying velocities, factor is 0.97857 Modifying velocities, factor is 0.93214 Modifying velocities, factor is 0.92763 Modifying velocities, factor is 0.93122 Modifying velocities, factor is 0.97325 Modifying velocities, factor is 1.08839 Modifying velocities, factor is 1.03669 Modifying velocities, factor is 1.07479 Modifying velocities, factor is 0.99193 Modifying velocities, factor is 1.07580 Modifying velocities, factor is 0.96674 Modifying velocities, factor is 0.96527 Modifying velocities, factor is 1.07215 Modifying velocities, factor is 1.02101 Modifying velocities, factor is 1.05502 Modifying velocities, factor is 1.01848 Modifying velocities, factor is 1.09883 Modifying velocities, factor is 1.09382 Modifying velocities, factor is 0.95347 Modifying velocities, factor is 1.04885 Modifying velocities, factor is 1.02699 Modifying velocities, factor is 1.04228 Modifying velocities, factor is 1.09277 Modifying velocities, factor is 0.99382 Modifying velocities, factor is 0.93484 Modifying velocities, factor is 0.93350 Modifying velocities, factor is 0.96995 Modifying velocities, factor is 0.94460 Modifying velocities, factor is 1.00761 Modifying velocities, factor is 0.92946 Modifying velocities, factor is 1.05078 Modifying velocities, factor is 1.07746 Modifying velocities, factor is 0.91722 Modifying velocities, factor is 0.95121 Modifying velocities, factor is 1.05471 Modifying velocities, factor is 1.03586 Modifying velocities, factor is 1.02373 Modifying velocities, factor is 1.01711 Modifying velocities, factor is 1.01845 Modifying velocities, factor is 0.99142 Modifying velocities, factor is 1.03235 Modifying velocities, factor is 1.06629 Modifying velocities, factor is 1.01654 Modifying velocities, factor is 0.96747 Modifying velocities, factor is 0.98342 Modifying velocities, factor is 1.02560 Modifying velocities, factor is 1.03673 Modifying velocities, factor is 1.05407 Modifying velocities, factor is 1.00467 Modifying velocities, factor is 1.02864 Modifying velocities, factor is 0.95219 Modifying velocities, factor is 1.07347 Modifying velocities, factor is 0.97568 Modifying velocities, factor is 0.94965 Modifying velocities, factor is 1.02628 Modifying velocities, factor is 0.90199 Modifying velocities, factor is 1.04889 Modifying velocities, factor is 1.03907 Modifying velocities, factor is 1.05531 Modifying velocities, factor is 0.96156 Modifying velocities, factor is 1.00769 Modifying velocities, factor is 1.00915 Modifying velocities, factor is 1.01276 Modifying velocities, factor is 1.04867 Modifying velocities, factor is 1.00409 Modifying velocities, factor is 1.06192 Modifying velocities, factor is 0.94753 Modifying velocities, factor is 0.91734 Modifying velocities, factor is 1.09964 Modifying velocities, factor is 0.95953 Modifying velocities, factor is 0.91839 Modifying velocities, factor is 1.05271 Modifying velocities, factor is 0.97475 Modifying velocities, factor is 0.94386 Modifying velocities, factor is 1.09583 Modifying velocities, factor is 1.00229 Modifying velocities, factor is 1.03116 Modifying velocities, factor is 1.09392 Modifying velocities, factor is 1.03238 Modifying velocities, factor is 1.06378 Modifying velocities, factor is 0.91970 Modifying velocities, factor is 0.99059 Modifying velocities, factor is 1.04054 Modifying velocities, factor is 0.99288 Modifying velocities, factor is 0.90226 Modifying velocities, factor is 1.04745 Modifying velocities, factor is 1.08827 Modifying velocities, factor is 1.00956 Modifying velocities, factor is 0.94833 Modifying velocities, factor is 1.06070 Modifying velocities, factor is 1.01454 Modifying velocities, factor is 0.91546 Modifying velocities, factor is 1.03416 Modifying velocities, factor is 0.94344 Modifying velocities, factor is 0.96181 Modifying velocities, factor is 1.04982 there were 1470 particles; currently 1598 particles there were 1382 nbonh bonds, now there are 1446 there were 88 nbona bonds, now there are 168 there were 0 nbper bonds, now there are 0 there were 229 ntheth angles, now there are 393 there were 125 ntheta angles, now there are 273 there were 0 ngper angles, now there are 0 there were 368 nphih torsions, now there are 672 there were 237 nphia torsions, now there are 609 there were 0 ndper torsions, now there are 0 processing exclusion list finished creating LES subspace Checking topology sizes against compiled limits add_les> ~ add_les> ~ the following line is required at the end add_les> *EOD Finished reading subspace definitions. Looking for unique atom and covalent types 3 1 1.09000000000000 85.0000000000000 2 1.09000000000000 340.000000000000 5 3 1.09000000000000 85.0000000000000 4 1.09000000000000 340.000000000000 7 5 1.01000000000000 108.500000000000 6 1.01000000000000 434.000000000000 5 7 1.09000000000000 68.0000000000000 3 8 1.09000000000000 68.0000000000000 7 9 1.01000000000000 86.8000000000000 9 10 0.957200000000000 553.000000000000 10 11 1.51360000000000 553.000000000000 bond with hydrogen: 11 MAX # ATOMS IN A SINGLE RESIDUE = 70 Writing coordinates to output file Writing velocities to output file Writing box coords and angles to output file Successful completion of ADDLES