-------------------------------------------------------------------------------- FILE ASSIGNMENT -------------------------------------------------------------------------------- Input file : small.inp Output file : small.out_GB000 Sidechain potential file : /users/czarek/UNRES/GIT/unres/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16- 10-8k SCp potential file : /users/czarek/UNRES/GIT/unres/PARAM/scp.parm Electrostatic potential file : /users/czarek/UNRES/GIT/unres/PARAM/electr_631Gdp.parm Cumulant coefficient file : /users/czarek/UNRES/GIT/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3 Torsional parameter file : /users/czarek/UNRES/GIT/unres/PARAM/torsion_631Gdp.parm Double torsional parameter file : /users/czarek/UNRES/GIT/unres/PARAM/torsion_double_631Gdp.parm SCCOR parameter file : /users/czarek/UNRES/GIT/unres/PARAM/sccor_pdb_shelly.dat Bond & inertia constant file : /users/czarek/UNRES/GIT/unres/PARAM/bond.parm Bending parameter file : /users/czarek/UNRES/GIT/unres/PARAM/thetaml.5parm Rotamer parameter file : /users/czarek/UNRES/GIT/unres/PARAM/scgauss.parm Threading database : /users/czarek/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 3.1 build 41 compiled Fri Feb 15 01:43:03 2013 compiled by czarek@piasek3 OS name: Linux OS release: 2.6.32-42-generic OS version: #96-Ubuntu SMP Wed Aug 15 19:37:37 UTC 2012 flags: INSTALL_DIR = /users/software/mpich-1.2.7p1_int... FC= ifort OPT = -O3 -ip -w 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 FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ... LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr... ARCH = LINUX PP = /lib/cpp -P object = unres.o arcos.o cartprint.o chainbuild... GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ... GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP... E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR... E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort... ++++ End of compile info ++++ Potential is GB , exponents are 6 12 Disulfide bridge parameters: S-S bridge energy: -5.50 d0cm: 3.78 akcm: 15.10 akth: 11.00 akct: 12.00 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70 MPI: node= 0 iseed(4)= 0 0 -16 -62756 ran_num 6.422640197456531E-013 RMSDBC = 3.0 RMSDBC1 = 0.5 RMSDBC1MAX = 1.5 DRMS = 0.1 RMSDBCM = 3.0 Time limit (min): 960.0 RESCALE_MODE 2 Library routine used to diagonalize matrices. =========================== Parameters of the MD run =========================== The units are: positions: angstrom, time: 48.9 fs velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2 energy: kcal/mol, temperature: K Number of time steps: 20000 Initial time step of numerical integration: 0.10000 natural units 4.89000 fs Maximum acceleration threshold to reduce the time step/increase split number: 5.00000 Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000 Maximum velocity threshold to reduce velocities: 20.00000 Frequency of property output: 1000 Frequency of coordinate output: 300 Berendsen bath calculation Temperature: 400.00000 Coupling constant (tau): 1.00000 Momenta will be reset at zero every 1000 steps ============================== End of MD run setup ============================= Energy-term weights (unscaled): WSCC= 1.000000 (SC-SC) WSCP= 2.794050 (SC-p) WELEC= 0.145810 (p-p electr) WVDWPP= 0.145810 (p-p VDW) WBOND= 1.000000 (stretching) WANG= 1.956840 (bending) WSCLOC= 0.170100 (SC local) WTOR= 2.046980 (torsional) WTORD= 1.696240 (double torsional) WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) WEL_LOC= 1.218370 (multi-body 3-rd order) WCORR4= 1.846150 (multi-body 4th order) WCORR5= 0.027300 (multi-body 5th order) WCORR6= 0.007410 (multi-body 6th order) WSCCOR= 1.000000 (back-scloc correlation) WTURN3= 2.913860 (turns, 3rd order) WTURN4= 0.731780 (turns, 4th order) WTURN6= 0.023910 (turns, 6th order) Hydrogen-bonding correlation between contact pairs of peptide groups Scaling factor of 1,4 SC-p interactions: 0.400 General scaling factor of SC-p interactions: 1.000 Energy-term weights (scaled): WSCC= 1.000000 (SC-SC) WSCP= 2.794050 (SC-p) WELEC= 0.117327 (p-p electr) WVDWPP= 0.145810 (p-p VDW) WBOND= 1.000000 (stretching) WANG= 1.956840 (bending) WSCLOC= 0.170100 (SC local) WTOR= 1.647115 (torsional) WTORD= 1.058472 (double torsional) WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) WEL_LOC= 0.760276 (multi-body 3-rd order) WCORR4= 0.874494 (multi-body 4th order) WCORR5= 0.009729 (multi-body 5th order) WCORR6= 0.001982 (multi-body 6th order) WSCCOR= 0.804656 (back-scloc correlatkion) WTURN3= 1.818280 (turns, 3rd order) WTURN4= 0.346633 (turns, 4th order) WTURN6= 0.006394 (turns, 6th order) Reference temperature for weights calculation: 300.000000000000 Parameters of the SS-bond potential: D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH 11.0000000000000 AKCT 12.0000000000000 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS 13.7000000000000 EBR -5.50000000000000 SS_DEPTH -6.90133843152500 HT 3.59866156847500 ITEL 1 10 1 2 9 1 3 9 1 4 9 1 5 1 1 6 9 1 7 9 1 8 9 1 9 9 1 10 9 1 11 9 1 12 9 1 13 9 1 14 1 1 15 9 1 16 9 1 17 9 1 ns= 2 iss: 5 14 nss= 0 ihpb,jhpb: Boundaries in phi angle sampling: GLY 1 -180.0 180.0 ALA 2 -180.0 180.0 ALA 3 -180.0 180.0 ALA 4 -180.0 180.0 CYS 5 -180.0 180.0 ALA 6 -180.0 180.0 ALA 7 -180.0 180.0 ALA 8 -180.0 180.0 ALA 9 -180.0 180.0 ALA 10 -180.0 180.0 ALA 11 -180.0 180.0 ALA 12 -180.0 180.0 ALA 13 -180.0 180.0 CYS 14 -180.0 180.0 ALA 15 -180.0 180.0 ALA 16 -180.0 180.0 ALA 17 -180.0 180.0 GLY 18 -180.0 180.0 NZ_START= 1 NZ_END= 18 IZ_SC= 0 Initial geometry will be read in. Geometry of the virtual chain. Res d Theta Gamma Dsc Alpha Beta GLY 1 0.000 0.000 0.000 0.000 0.000 0.000 ALA 2 3.800 0.000 0.000 0.743 110.000 -120.000 ALA 3 3.800 90.000 0.000 0.743 110.000 -120.000 ALA 4 3.800 90.000 180.000 0.743 110.000 -120.000 CYS 5 3.800 90.000 180.000 1.237 100.000 -120.000 ALA 6 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 7 3.800 90.000 180.000 0.743 100.000 -120.000 ALA 8 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 9 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 10 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 11 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000 CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000 ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000 ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000 GLY 18 3.800 90.000 180.000 0.000 0.000 0.000 The chain contains 2 disulfide-bridging cysteines. 5 14 Running with dynamic disulfide-bond formation Processor 0 CG group 0 absolute rank 0 nhpb 0 link_start= 1 link_end 0 ******************************************************************************** Processor 0: end reading molecular data. ******************************************************************************** Mesoscopic molecular dynamics (MD) calculation. ******************************************************************************** Calling chainbuild ====================MD calculation start==================== Initial velocities randomly generated Initial velocities 0 0.39133 0.02679 0.27319 0.00000 0.00000 0.00000 1 -0.17409 -0.26585 -0.21721 0.00000 0.00000 0.00000 2 -0.17148 0.42025 0.20576 -0.07613 0.16475 0.01193 3 -0.01404 -0.36110 -0.46494 -0.31406 0.04480 -0.30309 4 0.15172 0.29663 0.29266 -0.07974 0.11323 0.22586 5 -0.32168 -0.01456 0.05151 -0.17812 -0.01530 -0.02557 6 0.11448 0.13832 0.17223 -0.12900 -0.20376 -0.11786 7 -0.18175 -0.37828 -0.09633 -0.17966 -0.19816 -0.31341 8 -0.02028 0.22735 -0.36928 -0.04858 0.08355 -0.26764 9 0.34459 -0.25203 0.14694 0.01426 -0.12058 -0.21343 10 -0.41200 0.20762 -0.12944 -0.00588 -0.02316 0.01848 11 0.48857 -0.08617 0.25832 0.35227 -0.04402 0.04919 12 -0.32840 -0.19630 -0.27333 -0.07994 -0.13029 -0.14699 13 0.13872 0.24955 0.17068 0.08823 0.11539 0.21615 14 0.18253 0.02951 -0.14956 -0.11740 -0.10145 -0.17371 15 -0.19102 -0.09980 0.23974 0.03607 -0.01130 0.14715 16 0.08092 0.16784 -0.32778 0.01162 0.30480 -0.18318 17 -0.14311 -0.25973 0.34658 -0.44245 -0.17578 0.34891 18 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 Calling the zero-angular momentum subroutine vcm right after adjustment: 2.064717366521174E-017 -1.189837126469829E-017 5.249281440308069E-018 alpha-carbon coordinates centroid coordinates X Y Z X Y Z GLY( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ALA( 2) 3.80000 0.00000 0.00000 3.73284 0.42654 0.60465 ALA( 3) 3.80000 -3.80000 0.00000 3.37346 -3.73284 -0.60465 ALA( 4) 7.60000 -3.80000 0.00000 7.53284 -3.37346 0.60465 CYS( 5) 7.60000 -7.60000 0.00000 7.01741 -7.32119 -1.05500 ALA( 6) 11.40000 -7.60000 0.00000 11.33284 -7.17346 0.60465 ALA( 7) 11.40000 -11.40000 0.00000 11.05007 -11.23253 -0.63368 ALA( 8) 15.20000 -11.40000 0.00000 15.13284 -10.97346 0.60465 ALA( 9) 15.20000 -15.20000 0.00000 14.77346 -15.13284 -0.60465 ALA( 10) 19.00000 -15.20000 0.00000 18.93284 -14.77346 0.60465 ALA( 11) 19.00000 -19.00000 0.00000 18.57346 -18.93284 -0.60465 ALA( 12) 22.80000 -19.00000 0.00000 22.73284 -18.57346 0.60465 ALA( 13) 22.80000 -22.80000 0.00000 22.45007 -22.63253 -0.63368 CYS( 14) 26.60000 -22.80000 0.00000 26.48819 -22.08987 1.00667 ALA( 15) 26.60000 -26.60000 0.00000 26.25007 -26.43253 -0.63368 ALA( 16) 30.40000 -26.60000 0.00000 30.33284 -26.17346 0.60465 ALA( 17) 30.40000 -30.40000 0.00000 29.97346 -30.33284 -0.60465 GLY( 18) 34.20000 -30.40000 0.00000 34.20000 -30.40000 0.00000 Geometry of the virtual chain. Res d Theta Gamma Dsc Alpha Beta GLY 1 0.000 0.000 0.000 0.000 0.000 0.000 ALA 2 3.800 0.000 0.000 0.743 110.000 -120.000 ALA 3 3.800 90.000 0.000 0.743 110.000 -120.000 ALA 4 3.800 90.000 180.000 0.743 110.000 -120.000 CYS 5 3.800 90.000 180.000 1.237 100.000 -120.000 ALA 6 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 7 3.800 90.000 180.000 0.743 100.000 -120.000 ALA 8 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 9 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 10 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 11 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000 CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000 ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000 ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000 GLY 18 3.800 90.000 180.000 0.000 180.000 180.000 dyn_ssbond_ene -1.212205582757399E-004 Potential energy and its components Virtual-chain energies: EVDW= -1.784028E+01 WEIGHT= 1.000000E+00 (SC-SC) EVDW2= 2.118779E+01 WEIGHT= 2.794050E+00 (SC-p) EES= -8.122745E+00 WEIGHT= 1.173269E-01 (p-p) EVDWPP= -2.540621E+01 WEIGHT= 1.458100E-01 (p-p VDW) ESTR= 4.237046E-27 WEIGHT= 1.000000E+00 (stretching) EBE= -1.185178E+00 WEIGHT= 1.956840E+00 (bending) ESC= 1.520408E+02 WEIGHT= 1.701000E-01 (SC local) ETORS= 0.000000E+00 WEIGHT= 1.647115E+00 (torsional) ETORSD= -2.194244E+00 WEIGHT= 1.058472E+00 (double torsional) EHPB= 0.000000E+00 WEIGHT= 1.000000E+00 (SS bridges & dist. cnstr.) ECORR4= -5.324225E+00 WEIGHT= 8.744941E-01 (multi-body) ECORR5= 2.317900E+01 WEIGHT= 9.728750E-03 (multi-body) ECORR6= 1.215220E+01 WEIGHT= 1.981519E-03 (multi-body) EELLO= 3.759544E+01 WEIGHT= 7.602761E-01 (electrostatic-local) ETURN3= -3.193381E+00 WEIGHT= 1.818280E+00 (turns, 3rd order) ETURN4= 1.424793E+01 WEIGHT= 3.466334E-01 (turns, 4th order) ETURN6= 0.000000E+00 WEIGHT= 6.393807E-03 (turns, 6th order) ESCCOR= 7.779132E+00 WEIGHT= 8.046559E-01 (backbone-rotamer corr) EDIHC= 0.000000E+00 (dihedral angle constraints) ESS= 0.000000E+00 (disulfide-bridge intrinsic energy) UCONST= 0.000000E+00 (Constraint energy) ETOT= 8.749073E+01 (total) Initial: Kinetic energy 3.88148E+01 potential energy 8.74907E+01 total energy 1.26306E+02 maximum acceleration 4.30400E+00 dyn_ssbond_ene -1.225233984150210E-004 dyn_ssbond_ene -1.235216690847935E-004 dyn_ssbond_ene -1.239486545928095E-004 dyn_ssbond_ene -1.238584996470479E-004 dyn_ssbond_ene -1.235049382355485E-004 dyn_ssbond_ene -1.231647685385536E-004 dyn_ssbond_ene -1.230062098138728E-004 dyn_ssbond_ene -1.229989609355876E-004 dyn_ssbond_ene -1.229346445179793E-004 dyn_ssbond_ene -1.225841428541722E-004 dyn_ssbond_ene -1.218556109689701E-004 dyn_ssbond_ene -1.208085556834762E-004 dyn_ssbond_ene -1.195753331507502E-004 dyn_ssbond_ene -1.182910677035119E-004 dyn_ssbond_ene -1.170703501183243E-004 dyn_ssbond_ene -1.159781939346138E-004 dyn_ssbond_ene -1.149909845299786E-004 dyn_ssbond_ene -1.140050202876231E-004 dyn_ssbond_ene -1.129165586072755E-004 dyn_ssbond_ene -1.117002364424233E-004 dyn_ssbond_ene -1.104114488581961E-004 dyn_ssbond_ene -1.091309777487736E-004 dyn_ssbond_ene -1.079112548168324E-004 dyn_ssbond_ene -1.067758251304834E-004 dyn_ssbond_ene -1.057378087162563E-004 dyn_ssbond_ene -1.048132545435360E-004 dyn_ssbond_ene -1.040214904960590E-004 dyn_ssbond_ene -1.033726584909559E-004 dyn_ssbond_ene -1.028580302378407E-004 dyn_ssbond_ene -1.024500316990491E-004 dyn_ssbond_ene -1.021065226410818E-004 dyn_ssbond_ene -1.017850016815334E-004 dyn_ssbond_ene -1.014313798473377E-004 dyn_ssbond_ene -1.009943649555610E-004 dyn_ssbond_ene -1.004841765352956E-004 dyn_ssbond_ene -9.998766477934215E-005 dyn_ssbond_ene -9.959577657331249E-005 dyn_ssbond_ene -9.935395855652479E-005 dyn_ssbond_ene -9.925279117194036E-005 dyn_ssbond_ene -9.924822620794199E-005 dyn_ssbond_ene -9.927769175426951E-005 dyn_ssbond_ene -9.927135540676885E-005 dyn_ssbond_ene -9.918260020150128E-005 dyn_ssbond_ene -9.902463880553332E-005 dyn_ssbond_ene -9.887185742756106E-005 dyn_ssbond_ene -9.881488800782329E-005 dyn_ssbond_ene -9.890785110866551E-005 dyn_ssbond_ene -9.914471241051610E-005 dyn_ssbond_ene -9.946597434626823E-005 dyn_ssbond_ene -9.979298579725388E-005 dyn_ssbond_ene -1.000605873261375E-004 dyn_ssbond_ene -1.002289358858018E-004 dyn_ssbond_ene -1.002927476910725E-004 dyn_ssbond_ene -1.002772463385661E-004 dyn_ssbond_ene -1.002215913048937E-004 dyn_ssbond_ene -1.001580400496053E-004 dyn_ssbond_ene -1.000983110994047E-004 dyn_ssbond_ene -1.000363546141854E-004 dyn_ssbond_ene -9.996263042611374E-005 dyn_ssbond_ene -9.987224129023025E-005 dyn_ssbond_ene -9.976211934192423E-005 dyn_ssbond_ene -9.961438924337146E-005 dyn_ssbond_ene -9.939896994668520E-005 dyn_ssbond_ene -9.910315843837271E-005 dyn_ssbond_ene -9.875177841979965E-005 dyn_ssbond_ene -9.840240277248866E-005 dyn_ssbond_ene -9.812806188953262E-005 dyn_ssbond_ene -9.799278908183256E-005 dyn_ssbond_ene -9.801747874462502E-005 dyn_ssbond_ene -9.816490065600228E-005 dyn_ssbond_ene -9.835195194231482E-005 dyn_ssbond_ene -9.848381426888966E-005 dyn_ssbond_ene -9.849617524239850E-005 dyn_ssbond_ene -9.837795220710463E-005 dyn_ssbond_ene -9.816140973451940E-005 dyn_ssbond_ene -9.789319240940393E-005 dyn_ssbond_ene -9.760732575130924E-005 dyn_ssbond_ene -9.731535090644836E-005 dyn_ssbond_ene -9.701283331245719E-005 dyn_ssbond_ene -9.669283908489333E-005 dyn_ssbond_ene -9.635553135228092E-005 dyn_ssbond_ene -9.600750995488889E-005 dyn_ssbond_ene -9.565850510495793E-005 dyn_ssbond_ene -9.531774213146081E-005 dyn_ssbond_ene -9.498812068210155E-005 dyn_ssbond_ene -9.466157674614198E-005 dyn_ssbond_ene -9.432100600459947E-005 dyn_ssbond_ene -9.394885651608976E-005 dyn_ssbond_ene -9.353785679369713E-005 dyn_ssbond_ene -9.309025508181692E-005 dyn_ssbond_ene -9.353113843042627E-005 dyn_ssbond_ene -9.308394816492838E-005 dyn_ssbond_ene -9.352442629835200E-005 dyn_ssbond_ene -9.307755430545810E-005 dyn_ssbond_ene -9.351771892551675E-005 dyn_ssbond_ene -9.307108126716058E-005 dyn_ssbond_ene -9.351101498548866E-005 dyn_ssbond_ene -9.306453611527566E-005 dyn_ssbond_ene -9.350431328408699E-005 dyn_ssbond_ene -9.305792527430483E-005 dyn_ssbond_ene -9.349761274722128E-005 dyn_ssbond_ene -9.305125458212808E-005 dyn_ssbond_ene -9.349091240977738E-005 dyn_ssbond_ene -9.304452934025228E-005 dyn_ssbond_ene -9.348421140546223E-005 dyn_ssbond_ene -9.303775436039344E-005 dyn_ssbond_ene -9.347750895754473E-005 dyn_ssbond_ene -9.303093400761549E-005 dyn_ssbond_ene -9.347080437041695E-005 dyn_ssbond_ene -9.302407224005261E-005 dyn_ssbond_ene -9.346409702191539E-005 dyn_ssbond_ene -9.301717264548242E-005 dyn_ssbond_ene -9.345738635633444E-005 dyn_ssbond_ene -9.301023847486262E-005 dyn_ssbond_ene -9.345067187808121E-005 dyn_ssbond_ene -9.300327267312803E-005 dyn_ssbond_ene -9.344395314591053E-005 dyn_ssbond_ene -9.299627790730556E-005 dyn_ssbond_ene -9.343722976769420E-005 dyn_ssbond_ene -9.298925659224290E-005 dyn_ssbond_ene -9.343050139567810E-005 dyn_ssbond_ene -9.298221091397052E-005 dyn_ssbond_ene -9.342376772217917E-005 dyn_ssbond_ene -9.297514285134655E-005 dyn_ssbond_ene -9.341702847569117E-005 dyn_ssbond_ene -9.296805419497154E-005 dyn_ssbond_ene -9.341028341735278E-005 dyn_ssbond_ene -9.296094656549431E-005 dyn_ssbond_ene -9.340353233775144E-005 dyn_ssbond_ene -9.295382122546399E-005 dyn_ssbond_ene -9.339677505380065E-005 dyn_ssbond_ene -9.294667488588103E-005 dyn_ssbond_ene -9.339001140067946E-005 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dyn_ssbond_ene -2.767222096258478E-005 dyn_ssbond_ene -2.765169648544699E-005 dyn_ssbond_ene -2.761725582970220E-005 dyn_ssbond_ene -2.756647166728584E-005 dyn_ssbond_ene -2.749064868204018E-005 dyn_ssbond_ene -2.737225988300577E-005 dyn_ssbond_ene -2.719965659801594E-005 dyn_ssbond_ene -2.698629620546172E-005 dyn_ssbond_ene -2.677291977997626E-005 dyn_ssbond_ene -2.660598966314399E-005 dyn_ssbond_ene -2.650977585824063E-005 dyn_ssbond_ene -2.647451930108993E-005 dyn_ssbond_ene -2.646261908687320E-005 dyn_ssbond_ene -2.642861627427156E-005 Momenta zeroed out, time 1642.45 dyn_ssbond_ene -2.634787704243029E-005 =================================== Timing =================================== MD calculations setup: 7.81250E-03 Energy & gradient evaluation: 8.36719E+00 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 MD steps: 8.94141E+00 ============================ End of MD calculation =========================== CG processor 0 is finishing work. Total wall clock time 8.97656250000000 sec