-------------------------------------------------------------------------------- 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: 50000 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 0.000000000000000E+000 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 Pre-formed links are: ******************************************************************************** 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 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 4.30399E+00 Momenta zeroed out, time 89.72 Momenta zeroed out, time 184.80 Momenta zeroed out, time 255.62 Momenta zeroed out, time 334.60 Momenta zeroed out, time 415.00 Momenta zeroed out, time 498.96 Momenta zeroed out, time 586.14 Momenta zeroed out, time 675.88 Momenta zeroed out, time 766.19 Momenta zeroed out, time 847.02 Momenta zeroed out, time 934.67 Momenta zeroed out, time 1018.19 Momenta zeroed out, time 1112.72 Momenta zeroed out, time 1197.49 Momenta zeroed out, time 1281.88 Momenta zeroed out, time 1363.69 Momenta zeroed out, time 1440.30 Momenta zeroed out, time 1524.49 Momenta zeroed out, time 1613.51 Momenta zeroed out, time 1693.76 Momenta zeroed out, time 1784.30 Momenta zeroed out, time 1866.61 Momenta zeroed out, time 1957.29 Momenta zeroed out, time 2045.18 Momenta zeroed out, time 2132.51 Momenta zeroed out, time 2222.74 Momenta zeroed out, time 2308.03 Momenta zeroed out, time 2386.51 Momenta zeroed out, time 2465.39 Momenta zeroed out, time 2545.75 Momenta zeroed out, time 2626.03 Momenta zeroed out, time 2712.22 Momenta zeroed out, time 2790.06 Momenta zeroed out, time 2856.14 Momenta zeroed out, time 2935.37 Momenta zeroed out, time 3026.25 Momenta zeroed out, time 3115.49 Momenta zeroed out, time 3197.76 Momenta zeroed out, time 3280.83 Momenta zeroed out, time 3361.57 Momenta zeroed out, time 3435.50 Momenta zeroed out, time 3501.99 Momenta zeroed out, time 3588.70 Momenta zeroed out, time 3675.90 Momenta zeroed out, time 3760.47 Momenta zeroed out, time 3843.93 Momenta zeroed out, time 3930.62 Momenta zeroed out, time 4021.79 Momenta zeroed out, time 4102.92 Momenta zeroed out, time 4199.64 =================================== Timing =================================== MD calculations setup: 7.81250E-03 Energy & gradient evaluation: 2.00859E+01 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 MD steps: 2.13477E+01 ============================ End of MD calculation =========================== CG processor 0 is finishing work. Total wall clock time 21.3789062500000 sec