X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=examples%2Funres%2Fnew%2FREMD%2FNose-Hoover%2Fff_gab%2F1L2Y_REMD.out_GB000;h=9520de4ed0946ee42d890944f73f2bd5f39a6b96;hb=a006e7a005da9177ff9a9eab77e5b15cfcfb9fda;hp=08c17014239cf31f725201bc495cd841cab82b76;hpb=ed61b513686e36bded0e03e1e6e66d7d21d4981f;p=unres.git diff --git a/examples/unres/new/REMD/Nose-Hoover/ff_gab/1L2Y_REMD.out_GB000 b/examples/unres/new/REMD/Nose-Hoover/ff_gab/1L2Y_REMD.out_GB000 index 08c1701..9520de4 100644 --- a/examples/unres/new/REMD/Nose-Hoover/ff_gab/1L2Y_REMD.out_GB000 +++ b/examples/unres/new/REMD/Nose-Hoover/ff_gab/1L2Y_REMD.out_GB000 @@ -5,35 +5,41 @@ Output file : 1L2Y_REMD.out_GB000 Sidechain potential file : - /users/adam/unres//PARAM/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_gap8g-sc - SCp potential file : /users/adam/unres//PARAM/scp.parm - Electrostatic potential file : /users/adam/unres//PARAM/electr_631Gdp.parm + /users/pk376/unres-git/unres/PARAM/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_ga + p8g-sc + SCp potential file : /users/pk376/unres-git/unres/PARAM/scp.parm + Electrostatic potential file : + /users/pk376/unres-git/unres/PARAM/electr_631Gdp.parm Cumulant coefficient file : - /users/adam/unres//PARAM/fourier_opt.parm.1igd_hc_iter3_3 - Torsional parameter file : /users/adam/unres//PARAM/torsion_631Gdp.parm + /users/pk376/unres-git/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3 + Torsional parameter file : + /users/pk376/unres-git/unres/PARAM/torsion_631Gdp.parm Double torsional parameter file : - /users/adam/unres//PARAM/torsion_double_631Gdp.parm - SCCOR parameter file : /users/adam/unres//PARAM/rotcorr_AM1.parm - Bond & inertia constant file : /users/adam/unres//PARAM/bond.parm - Bending parameter file : /users/adam/unres//PARAM/thetaml.5parm - Rotamer parameter file : /users/adam/unres//PARAM/scgauss.parm - Threading database : /users/adam/unres//PARAM/patterns.cart + /users/pk376/unres-git/unres/PARAM/torsion_double_631Gdp.parm + SCCOR parameter file : /users/pk376/unres-git/unres/PARAM/sccor_pdb_shelly.dat + Bond & inertia constant file : /users/pk376/unres-git/unres/PARAM/bond.parm + Bending parameter file : + /users/pk376/unres-git/unres/PARAM/thetaml.5parm + Rotamer parameter file : + /users/pk376/unres-git/unres/PARAM/scgauss.parm + Threading database : + /users/pk376/unres-git/unres/PARAM/patterns.cart -------------------------------------------------------------------------------- ******************************************************************************** United-residue force field calculation - parallel job. ******************************************************************************** ### LAST MODIFIED 03/28/12 23:29 by czarek ++++ Compile info ++++ - Version 2.5 build 62 - compiled Sun May 13 16:07:22 2012 - compiled by adam@matrix.chem.cornell.edu + Version 2.5 build 302 + compiled Mon Jul 23 17:42:12 2012 + compiled by jal47@matrix.chem.cornell.edu OS name: Linux OS release: 2.6.34.9-69.fc13.x86_64 OS version: #1 SMP Tue May 3 09:23:03 UTC 2011 flags: INSTALL_DIR = /users/software/mpich-1.2.7p1_int... FC= ifort - OPT = -O3 -ip -w + OPT = -g -ip -w -CB FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)... FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include @@ -365,7 +371,7 @@ ndowna 16: 15 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 Calling the zero-angular momentum subroutine vcm right after adjustment: - -1.347581050579500E-017 1.082148419404750E-017 4.083578941150001E-018 + 2.286804207044001E-017 1.061730524699000E-017 -3.266863152920001E-018 alpha-carbon coordinates centroid coordinates @@ -452,22 +458,22 @@ Initial: maximum acceleration 7.10627E-01 - Setup time 1.562500000000000E-002 + Setup time 1.953125000000000E-002 REMD synchro at 100000 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 MIN ii_write= 1 - REMD gather times= 32.7773437500000 0.000000000000000E+000 + REMD gather times= 41.2968750000000 0.000000000000000E+000 REMD writing rst time= 3.906250000000000E-003 REMD writing traj time= 0.000000000000000E+000 NREP 16 ACC 1 250.00000 1.00000 1 ACC 2 260.00000 1.00000 1 -ACC 3 270.00000 1.00000 1 +ACC 3 270.00000 0.00000 1 ACC 4 280.00000 1.00000 1 ACC 5 290.00000 1.00000 1 ACC 6 300.00000 0.00000 1 -ACC 7 310.00000 0.00000 1 -ACC 8 320.00000 0.00000 1 +ACC 7 310.00000 1.00000 1 +ACC 8 320.00000 1.00000 1 ACC 9 330.00000 0.00000 1 ACC 10 340.00000 0.00000 1 ACC 11 350.00000 0.00000 1 @@ -477,248 +483,233 @@ ACC 14 380.00000 1.00000 1 ACC 15 390.00000 1.00000 1 REMD scatter time= 0.000000000000000E+000 REMD exchange time= 3.906250000000000E-003 - acceleration/energy drift too large 10.2692475218536 - 9.19801076866059 split increased to 2 itime 144660 - itsplit 1 REMD synchro at 200000 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 MIN ii_write= 1 - REMD gather times= 65.5507812500000 0.000000000000000E+000 - REMD writing rst time= 0.000000000000000E+000 + REMD gather times= 82.8515625000000 0.000000000000000E+000 + REMD writing rst time= 3.906250000000000E-003 REMD writing traj time= 3.906250000000000E-003 NREP 16 ACC 1 250.00000 0.50000 2 ACC 2 260.00000 0.50000 2 -ACC 3 270.00000 1.00000 2 +ACC 3 270.00000 0.00000 2 ACC 4 280.00000 1.00000 2 -ACC 5 290.00000 0.50000 2 +ACC 5 290.00000 1.00000 2 ACC 6 300.00000 0.50000 2 ACC 7 310.00000 0.50000 2 -ACC 8 320.00000 0.50000 2 +ACC 8 320.00000 1.00000 2 ACC 9 330.00000 0.00000 2 ACC 10 340.00000 0.50000 2 ACC 11 350.00000 0.50000 2 -ACC 12 360.00000 0.50000 2 +ACC 12 360.00000 1.00000 2 ACC 13 370.00000 1.00000 2 ACC 14 380.00000 1.00000 2 ACC 15 390.00000 1.00000 2 REMD scatter time= 0.000000000000000E+000 - REMD exchange time= 3.906250000000000E-003 - acceleration/energy drift too large 14.4778838599469 - 22.1867930678403 split increased to 2 itime 216480 + REMD exchange time= 7.812500000000000E-003 + acceleration/energy drift too large 11.7947192637743 + 12.6185934898872 split increased to 2 itime 205273 itsplit 1 REMD synchro at 300000 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 MIN ii_write= 1 - REMD gather times= 98.2890625000000 0.000000000000000E+000 + REMD gather times= 125.027343750000 0.000000000000000E+000 REMD writing rst time= 3.906250000000000E-003 REMD writing traj time= 0.000000000000000E+000 NREP 16 ACC 1 250.00000 0.33333 3 -ACC 2 260.00000 0.66667 3 -ACC 3 270.00000 1.00000 3 -ACC 4 280.00000 0.66667 3 +ACC 2 260.00000 0.33333 3 +ACC 3 270.00000 0.33333 3 +ACC 4 280.00000 1.00000 3 ACC 5 290.00000 0.66667 3 -ACC 6 300.00000 0.66667 3 +ACC 6 300.00000 0.33333 3 ACC 7 310.00000 0.66667 3 ACC 8 320.00000 0.66667 3 -ACC 9 330.00000 0.00000 3 +ACC 9 330.00000 0.33333 3 ACC 10 340.00000 0.66667 3 ACC 11 350.00000 0.66667 3 -ACC 12 360.00000 0.66667 3 -ACC 13 370.00000 1.00000 3 +ACC 12 360.00000 1.00000 3 +ACC 13 370.00000 0.66667 3 ACC 14 380.00000 0.66667 3 -ACC 15 390.00000 0.66667 3 - REMD scatter time= 3.906250000000000E-003 - REMD exchange time= 7.812500000000000E-003 - acceleration/energy drift too large 13.5949337110146 - 17.1429155690109 split increased to 2 itime 382676 +ACC 15 390.00000 1.00000 3 + REMD scatter time= 0.000000000000000E+000 + REMD exchange time= 3.906250000000000E-003 + acceleration/energy drift too large 11.2341422335143 + 16.0955510188413 split increased to 2 itime 348226 itsplit 1 REMD synchro at 400000 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 MIN ii_write= 1 - REMD gather times= 131.164062500000 0.000000000000000E+000 + REMD gather times= 166.632812500000 0.000000000000000E+000 REMD writing rst time= 3.906250000000000E-003 REMD writing traj time= 0.000000000000000E+000 NREP 16 ACC 1 250.00000 0.25000 4 -ACC 2 260.00000 0.75000 4 -ACC 3 270.00000 0.75000 4 -ACC 4 280.00000 0.75000 4 -ACC 5 290.00000 0.50000 4 -ACC 6 300.00000 0.75000 4 -ACC 7 310.00000 0.75000 4 +ACC 2 260.00000 0.25000 4 +ACC 3 270.00000 0.25000 4 +ACC 4 280.00000 1.00000 4 +ACC 5 290.00000 0.75000 4 +ACC 6 300.00000 0.50000 4 +ACC 7 310.00000 0.50000 4 ACC 8 320.00000 0.50000 4 -ACC 9 330.00000 0.25000 4 +ACC 9 330.00000 0.50000 4 ACC 10 340.00000 0.75000 4 ACC 11 350.00000 0.75000 4 -ACC 12 360.00000 0.50000 4 -ACC 13 370.00000 1.00000 4 +ACC 12 360.00000 1.00000 4 +ACC 13 370.00000 0.75000 4 ACC 14 380.00000 0.75000 4 -ACC 15 390.00000 0.75000 4 +ACC 15 390.00000 1.00000 4 REMD scatter time= 0.000000000000000E+000 REMD exchange time= 3.906250000000000E-003 - acceleration/energy drift too large 9.21361849793341 - 10.8677442555886 split increased to 2 itime 406798 - itsplit 1 - acceleration/energy drift too large 11.4661661903248 - 11.3565746853763 split increased to 2 itime 431285 - itsplit 1 - acceleration/energy drift too large 9.12510327664018 - 11.8795729175046 split increased to 2 itime 453653 + acceleration/energy drift too large 11.1581687600111 + 11.8937809741821 split increased to 2 itime 450747 itsplit 1 REMD synchro at 500000 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 MIN ii_write= 1 - REMD gather times= 164.027343750000 0.000000000000000E+000 - REMD writing rst time= 3.906250000000000E-003 + REMD gather times= 208.304687500000 0.000000000000000E+000 + REMD writing rst time= 0.000000000000000E+000 REMD writing traj time= 3.906250000000000E-003 NREP 16 -ACC 1 250.00000 0.20000 5 -ACC 2 260.00000 0.80000 5 -ACC 3 270.00000 0.80000 5 -ACC 4 280.00000 0.60000 5 -ACC 5 290.00000 0.60000 5 -ACC 6 300.00000 0.80000 5 -ACC 7 310.00000 0.80000 5 -ACC 8 320.00000 0.40000 5 +ACC 1 250.00000 0.40000 5 +ACC 2 260.00000 0.20000 5 +ACC 3 270.00000 0.20000 5 +ACC 4 280.00000 0.80000 5 +ACC 5 290.00000 0.80000 5 +ACC 6 300.00000 0.60000 5 +ACC 7 310.00000 0.40000 5 +ACC 8 320.00000 0.60000 5 ACC 9 330.00000 0.40000 5 ACC 10 340.00000 0.80000 5 -ACC 11 350.00000 0.60000 5 -ACC 12 360.00000 0.60000 5 -ACC 13 370.00000 1.00000 5 -ACC 14 380.00000 0.60000 5 +ACC 11 350.00000 0.80000 5 +ACC 12 360.00000 1.00000 5 +ACC 13 370.00000 0.80000 5 +ACC 14 380.00000 0.80000 5 ACC 15 390.00000 0.80000 5 REMD scatter time= 0.000000000000000E+000 - REMD exchange time= 7.812500000000000E-003 - acceleration/energy drift too large 13.5831722409554 - 18.1557409044710 split increased to 2 itime 521515 - itsplit 1 - acceleration/energy drift too large 10.8154809994798 - 11.2590526452597 split increased to 2 itime 555749 + REMD exchange time= 3.906250000000000E-003 + acceleration/energy drift too large 11.9473386275269 + 16.6003287460296 split increased to 2 itime 529448 itsplit 1 - acceleration/energy drift too large 9.87865643855208 - 11.2237001105368 split increased to 2 itime 575938 + acceleration/energy drift too large 10.7642600253068 + 13.4561498306359 split increased to 2 itime 578217 itsplit 1 REMD synchro at 600000 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 MIN ii_write= 1 - REMD gather times= 198.058593750000 0.000000000000000E+000 + REMD gather times= 250.296875000000 0.000000000000000E+000 REMD writing rst time= 3.906250000000000E-003 - REMD writing traj time= 3.906250000000000E-003 + REMD writing traj time= 0.000000000000000E+000 NREP 16 -ACC 1 250.00000 0.16667 6 -ACC 2 260.00000 0.66667 6 -ACC 3 270.00000 0.66667 6 -ACC 4 280.00000 0.50000 6 -ACC 5 290.00000 0.50000 6 -ACC 6 300.00000 0.83333 6 -ACC 7 310.00000 0.66667 6 -ACC 8 320.00000 0.50000 6 -ACC 9 330.00000 0.50000 6 -ACC 10 340.00000 0.83333 6 -ACC 11 350.00000 0.50000 6 -ACC 12 360.00000 0.66667 6 +ACC 1 250.00000 0.50000 6 +ACC 2 260.00000 0.33333 6 +ACC 3 270.00000 0.16667 6 +ACC 4 280.00000 0.83333 6 +ACC 5 290.00000 0.66667 6 +ACC 6 300.00000 0.50000 6 +ACC 7 310.00000 0.50000 6 +ACC 8 320.00000 0.66667 6 +ACC 9 330.00000 0.33333 6 +ACC 10 340.00000 0.66667 6 +ACC 11 350.00000 0.83333 6 +ACC 12 360.00000 1.00000 6 ACC 13 370.00000 0.83333 6 -ACC 14 380.00000 0.66667 6 +ACC 14 380.00000 0.83333 6 ACC 15 390.00000 0.83333 6 REMD scatter time= 0.000000000000000E+000 - REMD exchange time= 7.812500000000000E-003 - acceleration/energy drift too large 10.1405477752545 - 14.0455054892036 split increased to 2 itime 651174 - itsplit 1 + REMD exchange time= 3.906250000000000E-003 REMD synchro at 700000 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 MIN ii_write= 1 - REMD gather times= 231.082031250000 0.000000000000000E+000 + REMD gather times= 291.777343750000 0.000000000000000E+000 REMD writing rst time= 3.906250000000000E-003 REMD writing traj time= 0.000000000000000E+000 NREP 16 -ACC 1 250.00000 0.28571 7 -ACC 2 260.00000 0.57143 7 -ACC 3 270.00000 0.57143 7 -ACC 4 280.00000 0.42857 7 +ACC 1 250.00000 0.57143 7 +ACC 2 260.00000 0.42857 7 +ACC 3 270.00000 0.14286 7 +ACC 4 280.00000 0.71429 7 ACC 5 290.00000 0.57143 7 -ACC 6 300.00000 0.85714 7 -ACC 7 310.00000 0.57143 7 -ACC 8 320.00000 0.42857 7 -ACC 9 330.00000 0.57143 7 +ACC 6 300.00000 0.57143 7 +ACC 7 310.00000 0.42857 7 +ACC 8 320.00000 0.71429 7 +ACC 9 330.00000 0.42857 7 ACC 10 340.00000 0.71429 7 -ACC 11 350.00000 0.57143 7 -ACC 12 360.00000 0.71429 7 +ACC 11 350.00000 0.71429 7 +ACC 12 360.00000 1.00000 7 ACC 13 370.00000 0.85714 7 -ACC 14 380.00000 0.71429 7 -ACC 15 390.00000 0.85714 7 +ACC 14 380.00000 0.85714 7 +ACC 15 390.00000 0.71429 7 REMD scatter time= 0.000000000000000E+000 - REMD exchange time= 3.906250000000000E-003 - acceleration/energy drift too large 8.23162588035763 - 10.7407015461566 split increased to 2 itime 722736 + REMD exchange time= 7.812500000000000E-003 + acceleration/energy drift too large 10.7793195017638 + 13.5481889000988 split increased to 2 itime 789154 itsplit 1 REMD synchro at 800000 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 MIN ii_write= 1 - REMD gather times= 263.644531250000 0.000000000000000E+000 + REMD gather times= 333.242187500000 0.000000000000000E+000 REMD writing rst time= 3.906250000000000E-003 REMD writing traj time= 0.000000000000000E+000 NREP 16 -ACC 1 250.00000 0.25000 8 -ACC 2 260.00000 0.62500 8 -ACC 3 270.00000 0.50000 8 -ACC 4 280.00000 0.50000 8 +ACC 1 250.00000 0.62500 8 +ACC 2 260.00000 0.50000 8 +ACC 3 270.00000 0.25000 8 +ACC 4 280.00000 0.62500 8 ACC 5 290.00000 0.62500 8 -ACC 6 300.00000 0.75000 8 -ACC 7 310.00000 0.62500 8 -ACC 8 320.00000 0.37500 8 -ACC 9 330.00000 0.50000 8 -ACC 10 340.00000 0.62500 8 -ACC 11 350.00000 0.62500 8 -ACC 12 360.00000 0.75000 8 -ACC 13 370.00000 0.87500 8 -ACC 14 380.00000 0.75000 8 -ACC 15 390.00000 0.87500 8 +ACC 6 300.00000 0.62500 8 +ACC 7 310.00000 0.50000 8 +ACC 8 320.00000 0.62500 8 +ACC 9 330.00000 0.37500 8 +ACC 10 340.00000 0.75000 8 +ACC 11 350.00000 0.75000 8 +ACC 12 360.00000 1.00000 8 +ACC 13 370.00000 0.75000 8 +ACC 14 380.00000 0.87500 8 +ACC 15 390.00000 0.75000 8 REMD scatter time= 0.000000000000000E+000 REMD exchange time= 3.906250000000000E-003 - acceleration/energy drift too large 13.8949382919279 - 21.6043010255298 split increased to 2 itime 858374 + acceleration/energy drift too large 9.66071688513195 + 12.0796171071504 split increased to 2 itime 833577 itsplit 1 REMD synchro at 900000 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 MIN ii_write= 1 - REMD gather times= 296.550781250000 0.000000000000000E+000 - REMD writing rst time= 0.000000000000000E+000 + REMD gather times= 375.066406250000 0.000000000000000E+000 + REMD writing rst time= 3.906250000000000E-003 REMD writing traj time= 3.906250000000000E-003 NREP 16 -ACC 1 250.00000 0.22222 9 -ACC 2 260.00000 0.66667 9 -ACC 3 270.00000 0.55556 9 -ACC 4 280.00000 0.44444 9 -ACC 5 290.00000 0.66667 9 -ACC 6 300.00000 0.77778 9 -ACC 7 310.00000 0.55556 9 -ACC 8 320.00000 0.33333 9 -ACC 9 330.00000 0.55556 9 -ACC 10 340.00000 0.55556 9 -ACC 11 350.00000 0.66667 9 -ACC 12 360.00000 0.77778 9 -ACC 13 370.00000 0.88889 9 -ACC 14 380.00000 0.77778 9 -ACC 15 390.00000 0.88889 9 +ACC 1 250.00000 0.66667 9 +ACC 2 260.00000 0.44444 9 +ACC 3 270.00000 0.33333 9 +ACC 4 280.00000 0.66667 9 +ACC 5 290.00000 0.55556 9 +ACC 6 300.00000 0.66667 9 +ACC 7 310.00000 0.44444 9 +ACC 8 320.00000 0.66667 9 +ACC 9 330.00000 0.44444 9 +ACC 10 340.00000 0.66667 9 +ACC 11 350.00000 0.77778 9 +ACC 12 360.00000 0.88889 9 +ACC 13 370.00000 0.77778 9 +ACC 14 380.00000 0.88889 9 +ACC 15 390.00000 0.77778 9 REMD scatter time= 0.000000000000000E+000 - REMD exchange time= 3.906250000000000E-003 - acceleration/energy drift too large 9.17292539795275 - 11.2544574789226 split increased to 2 itime 916641 + REMD exchange time= 7.812500000000000E-003 + acceleration/energy drift too large 12.3943859835290 + 15.4572766810046 split increased to 2 itime 946232 itsplit 1 - acceleration/energy drift too large 10.4284087174099 - 13.3595980214727 split increased to 2 itime 949590 + acceleration/energy drift too large 10.5294013063566 + 33.6470754235687 split increased to 2 itime 960546 itsplit 1 - acceleration/energy drift too large 12.0116953600714 - 18.1187559464182 split increased to 2 itime 967312 + acceleration/energy drift too large 9.09627417363667 + 10.9619024170769 split increased to 2 itime 972893 itsplit 1 - acceleration/energy drift too large 9.02648828637489 - 13.7756790232264 split increased to 2 itime 972032 + acceleration/energy drift too large 10.8429639456552 + 15.8998725659601 split increased to 2 itime 985022 itsplit 1 - acceleration/energy drift too large 10.6947954889208 - 13.0967923555457 split increased to 2 itime 976695 + acceleration/energy drift too large 9.22390726200052 + 25.4291482188530 split increased to 2 itime 993966 itsplit 1 REMD synchro at 1000000 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 @@ -728,13 +719,13 @@ ACC 15 390.00000 0.88889 9 =================================== Timing =================================== - MD calculations setup: 3.90625E-03 - Energy & gradient evaluation: 3.05223E+02 + MD calculations setup: 7.81250E-03 + Energy & gradient evaluation: 3.81410E+02 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 - MD steps: 3.29453E+02 + MD steps: 4.19094E+02 ============================ End of MD calculation =========================== CG processor 0 is finishing work. - Total wall clock time 329.468750000000 sec + Total wall clock time 419.113281250000 sec