X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=examples%2Funres%2Fnew%2FMD%2FNose_Hoover%2Fff_gab%2F1L2Y_MD.out_GB000;h=370b3795b7913e0548424d72a347197d74896bcf;hb=a006e7a005da9177ff9a9eab77e5b15cfcfb9fda;hp=c632ad7d0ed07bf42bd977dd1a97b831139cbd65;hpb=ed61b513686e36bded0e03e1e6e66d7d21d4981f;p=unres.git diff --git a/examples/unres/new/MD/Nose_Hoover/ff_gab/1L2Y_MD.out_GB000 b/examples/unres/new/MD/Nose_Hoover/ff_gab/1L2Y_MD.out_GB000 index c632ad7..370b379 100644 --- a/examples/unres/new/MD/Nose_Hoover/ff_gab/1L2Y_MD.out_GB000 +++ b/examples/unres/new/MD/Nose_Hoover/ff_gab/1L2Y_MD.out_GB000 @@ -5,35 +5,41 @@ Output file : 1L2Y_MD.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 @@ -304,7 +310,7 @@ Mesoscopic molecular dynamics (MD) calculation. 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 Calling the zero-angular momentum subroutine vcm right after adjustment: - 3.226027363508501E-017 2.674744206453251E-017 6.125368411725002E-018 + 1.837610523517500E-017 -2.960594732333751E-018 9.596410511702503E-018 alpha-carbon coordinates centroid coordinates @@ -391,50 +397,65 @@ Initial: maximum acceleration 7.07629E-01 - acceleration/energy drift too large 9.78013718448949 - 10.6971139128278 split increased to 2 itime 72745 + acceleration/energy drift too large 11.2926424070625 + 13.6605134887925 split increased to 2 itime 5488 itsplit 1 - acceleration/energy drift too large 6.65467285428532 - 11.4261305813792 split increased to 2 itime 213434 + acceleration/energy drift too large 12.2479155916642 + 17.8916022742654 split increased to 2 itime 146134 itsplit 1 - acceleration/energy drift too large 6.23173521323265 - 12.7765218283068 split increased to 2 itime 224643 + acceleration/energy drift too large 9.64402968286842 + 11.3087438689470 split increased to 2 itime 173097 itsplit 1 - acceleration/energy drift too large 9.82326621220746 - 10.5112359366962 split increased to 2 itime 240810 + acceleration/energy drift too large 5.98151849708125 + 10.5358868963268 split increased to 2 itime 325094 itsplit 1 - acceleration/energy drift too large 11.6741711355468 - 14.5266567820789 split increased to 2 itime 293410 + acceleration/energy drift too large 9.92185743247020 + 10.3282402848183 split increased to 2 itime 337991 itsplit 1 - acceleration/energy drift too large 14.4639213800120 - 23.7234928069806 split increased to 2 itime 413671 + acceleration/energy drift too large 12.4467738353776 + 16.3475089599066 split increased to 2 itime 377718 itsplit 1 - acceleration/energy drift too large 10.7495418233675 - 11.7766241585679 split increased to 2 itime 707772 + acceleration/energy drift too large 9.40536271695775 + 11.7402473647113 split increased to 2 itime 399086 itsplit 1 - acceleration/energy drift too large 14.1580222958177 - 15.5950126123075 split increased to 2 itime 782746 + acceleration/energy drift too large 13.1653706876790 + 16.9150100267623 split increased to 2 itime 448471 itsplit 1 - acceleration/energy drift too large 11.1422328063867 - 12.5552272072498 split increased to 2 itime 851609 + acceleration/energy drift too large 6.46490539699288 + 12.1544022140714 split increased to 2 itime 477390 itsplit 1 - acceleration/energy drift too large 7.92906617031973 - 14.0128676820342 split increased to 2 itime 904403 + acceleration/energy drift too large 13.1589518405409 + 17.5436060457116 split increased to 2 itime 479111 itsplit 1 - acceleration/energy drift too large 10.7058448136198 - 14.3424550573967 split increased to 2 itime 908867 + acceleration/energy drift too large 10.5950744430222 + 10.4028358818328 split increased to 2 itime 479526 + itsplit 1 + acceleration/energy drift too large 11.0521089342970 + 12.3123692023542 split increased to 2 itime 710277 + itsplit 1 + acceleration/energy drift too large 5.83156435721131 + 10.6993564628405 split increased to 2 itime 739656 + itsplit 1 + acceleration/energy drift too large 7.08760014331940 + 11.9290942024338 split increased to 2 itime 774367 + itsplit 1 + acceleration/energy drift too large 12.2797621496046 + 17.4776170393841 split increased to 2 itime 906363 + itsplit 1 + acceleration/energy drift too large 15.5956529698596 + 21.6103248292573 split increased to 2 itime 977004 itsplit 1 =================================== Timing =================================== MD calculations setup: 3.90625E-03 - Energy & gradient evaluation: 3.09223E+02 + Energy & gradient evaluation: 3.74867E+02 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 - MD steps: 3.28801E+02 + MD steps: 4.11719E+02 ============================ End of MD calculation =========================== CG processor 0 is finishing work. - Total wall clock time 333.972656250000 sec + Total wall clock time 420.156250000000 sec