-------------------------------------------------------------------------------- FILE ASSIGNMENT -------------------------------------------------------------------------------- Input file : 1L2Y_REMD.inp Output file : 1L2Y_REMD.out_GB000 Sidechain potential file : /users/pk376/unres-git/unres/PARAM/scinter_GB.parm 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/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/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_AM1.parm Bending parameter file : /users/pk376/unres-git/unres/PARAM/theta_abinitio.parm Rotamer parameter file : /users/pk376/unres-git/unres/PARAM/rotamers_AM1_aura.10022007.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 303 compiled Mon Jul 23 17:44:56 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 = -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 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 ++++ Start reading THETA_PDB End reading THETA_PDB 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 -46 -45086 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: 1000000 Initial time step of numerical integration: 0.20000 natural units 9.78000 fs A-MTS algorithm used; initial time step for fast-varying short-range forces split into 1 steps. Short-range force cutoff 2.00 lambda 0.30 Maximum acceleration threshold to reduce the time step/increase split number: 10.00000 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: 10000 Frequency of coordinate output: 10000 Berendsen bath calculation Temperature: 300.00000 Coupling constant (tau): 1.00000 Momenta will be reset at zero every 1000 steps Velocities will be reset at random every 10000 steps ============================== End of MD run setup ============================= REMD setup NREP= 16 NSTEX= 100000 SYNC= T NSYN= 100000 TRAJCACHE= 1 tlist 250.000000000000 260.000000000000 270.000000000000 280.000000000000 290.000000000000 300.000000000000 310.000000000000 320.000000000000 330.000000000000 340.000000000000 350.000000000000 360.000000000000 370.000000000000 380.000000000000 390.000000000000 400.000000000000 mlist 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Total number of replicas 16 ============================== End of REMD run setup ============================= Energy-term weights (unscaled): WSCC= 1.000000 (SC-SC) WSCP= 1.233150 (SC-p) WELEC= 0.844760 (p-p electr) WVDWPP= 0.231730 (p-p VDW) WBOND= 1.000000 (stretching) WANG= 0.629540 (bending) WSCLOC= 0.105540 (SC local) WTOR= 1.843160 (torsional) WTORD= 1.265710 (double torsional) WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) WEL_LOC= 0.373570 (multi-body 3-rd order) WCORR4= 0.192120 (multi-body 4th order) WCORR5= 0.000000 (multi-body 5th order) WCORR6= 0.000000 (multi-body 6th order) WSCCOR= 0.000000 (back-scloc correlation) WTURN3= 1.403230 (turns, 3rd order) WTURN4= 0.646730 (turns, 4th order) WTURN6= 0.000000 (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= 1.233150 (SC-p) WELEC= 0.844760 (p-p electr) WVDWPP= 0.231730 (p-p VDW) WBOND= 1.000000 (stretching) WANG= 0.629540 (bending) WSCLOC= 0.105540 (SC local) WTOR= 1.843160 (torsional) WTORD= 1.265710 (double torsional) WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) WEL_LOC= 0.373570 (multi-body 3-rd order) WCORR4= 0.192120 (multi-body 4th order) WCORR5= 0.000000 (multi-body 5th order) WCORR6= 0.000000 (multi-body 6th order) WSCCOR= 0.000000 (back-scloc correlatkion) WTURN3= 1.403230 (turns, 3rd order) WTURN4= 0.646730 (turns, 4th order) WTURN6= 0.000000 (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 PDB data will be read from file ../../../../1L2Y.pdb Nres: 21 Backbone and SC coordinates as read from the PDB 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754 nsup= 20 nstart_sup= 2 ITEL 1 21 0 2 14 1 3 5 1 4 8 1 5 4 1 6 13 1 7 7 1 8 5 1 9 19 1 10 16 1 11 10 1 12 10 2 13 20 1 14 12 1 15 12 1 16 10 1 17 18 2 18 20 2 19 20 2 20 20 1 21 12 0 ns= 0 iss: Boundaries in phi angle sampling: D 1 -180.0 180.0 ASN 2 -180.0 180.0 LEU 3 -180.0 180.0 TYR 4 -180.0 180.0 ILE 5 -180.0 180.0 GLN 6 -180.0 180.0 TRP 7 -180.0 180.0 LEU 8 -180.0 180.0 LYS 9 -180.0 180.0 ASP 10 -180.0 180.0 GLY 11 -180.0 180.0 GLY 12 -180.0 180.0 PRO 13 -180.0 180.0 SER 14 -180.0 180.0 SER 15 -180.0 180.0 GLY 16 -180.0 180.0 ARG 17 -180.0 180.0 PRO 18 -180.0 180.0 PRO 19 -180.0 180.0 PRO 20 -180.0 180.0 SER 21 -180.0 180.0 D 22 -180.0 180.0 nsup= 20 nsup= 20 nstart_sup= 2 nstart_seq= 2 NZ_START= 2 NZ_END= 21 IZ_SC= 0 Contact order: 0.308441558441558 Shifting contacts: 2 2 1 ILE 5 ASN 2 2 TRP 7 TYR 4 3 LEU 8 TYR 4 4 LEU 8 ILE 5 5 LYS 9 GLN 6 6 GLY 12 TRP 7 7 GLY 12 LEU 8 8 SER 14 GLY 11 9 SER 15 ASP 10 10 SER 15 GLY 11 11 PRO 19 TRP 7 12 PRO 20 LEU 3 13 PRO 20 TYR 4 14 PRO 20 TRP 7 j 2 k 3 +dist.constr 1 2 3 3.88 3.70E-02 j 2 k 4 +dist.constr 2 2 4 5.58 2.68E-02 j 2 k 5 +dist.constr 3 2 5 5.04 3.01E-02 j 2 k 6 +dist.constr 4 2 6 6.32 2.25E-02 j 2 k 7 +dist.constr 5 2 7 8.77 1.07E-02 j 2 k 8 +dist.constr 6 2 8 9.91 7.02E-03 j 2 k 9 +dist.constr 7 2 9 10.61 5.25E-03 j 2 k 10 +dist.constr 8 2 10 12.89 1.80E-03 j 3 k 4 +dist.constr 9 3 4 3.86 3.71E-02 j 3 k 5 +dist.constr 10 3 5 5.48 2.74E-02 j 3 k 6 +dist.constr 11 3 6 5.24 2.89E-02 j 3 k 7 +dist.constr 12 3 7 6.43 2.19E-02 j 3 k 8 +dist.constr 13 3 8 8.85 1.04E-02 j 3 k 9 +dist.constr 14 3 9 10.21 6.21E-03 j 3 k 10 +dist.constr 15 3 10 11.39 3.74E-03 j 4 k 5 +dist.constr 16 4 5 3.87 3.70E-02 j 4 k 6 +dist.constr 17 4 6 5.41 2.78E-02 j 4 k 7 +dist.constr 18 4 7 4.91 3.09E-02 j 4 k 8 +dist.constr 19 4 8 6.11 2.37E-02 j 4 k 9 +dist.constr 20 4 9 8.65 1.12E-02 j 4 k 10 +dist.constr 21 4 10 10.11 6.47E-03 j 5 k 6 +dist.constr 22 5 6 3.85 3.72E-02 j 5 k 7 +dist.constr 23 5 7 5.39 2.80E-02 j 5 k 8 +dist.constr 24 5 8 5.08 2.99E-02 j 5 k 9 +dist.constr 25 5 9 6.11 2.37E-02 j 5 k 10 +dist.constr 26 5 10 8.79 1.07E-02 j 6 k 7 +dist.constr 27 6 7 3.87 3.71E-02 j 6 k 8 +dist.constr 28 6 8 5.61 2.67E-02 j 6 k 9 +dist.constr 29 6 9 5.36 2.82E-02 j 6 k 10 +dist.constr 30 6 10 6.73 2.02E-02 j 7 k 8 +dist.constr 31 7 8 3.86 3.71E-02 j 7 k 9 +dist.constr 32 7 9 5.70 2.61E-02 j 7 k 10 +dist.constr 33 7 10 5.59 2.68E-02 j 8 k 9 +dist.constr 34 8 9 3.88 3.70E-02 j 8 k 10 +dist.constr 35 8 10 5.38 2.80E-02 j 9 k 10 +dist.constr 36 9 10 3.86 3.71E-02 +dist.constr 1 2 3 3.88 0.00 0 0.0 +dist.constr 2 2 4 5.58 0.00 0 0.0 +dist.constr 3 2 5 5.04 0.00 0 0.0 +dist.constr 4 2 6 6.32 0.00 0 0.0 +dist.constr 5 2 7 8.77 0.00 0 0.0 +dist.constr 6 2 8 9.91 0.00 0 0.0 +dist.constr 7 2 9 10.61 0.00 0 0.0 +dist.constr 8 2 10 12.89 0.00 0 0.0 +dist.constr 9 3 4 3.86 0.00 0 0.0 +dist.constr 10 3 5 5.48 0.00 0 0.0 +dist.constr 11 3 6 5.24 0.00 0 0.0 +dist.constr 12 3 7 6.43 0.00 0 0.0 +dist.constr 13 3 8 8.85 0.00 0 0.0 +dist.constr 14 3 9 10.21 0.00 0 0.0 +dist.constr 15 3 10 11.39 0.00 0 0.0 +dist.constr 16 4 5 3.87 0.00 0 0.0 +dist.constr 17 4 6 5.41 0.00 0 0.0 +dist.constr 18 4 7 4.91 0.00 0 0.0 +dist.constr 19 4 8 6.11 0.00 0 0.0 +dist.constr 20 4 9 8.65 0.00 0 0.0 +dist.constr 21 4 10 10.11 0.00 0 0.0 +dist.constr 22 5 6 3.85 0.00 0 0.0 +dist.constr 23 5 7 5.39 0.00 0 0.0 +dist.constr 24 5 8 5.08 0.00 0 0.0 +dist.constr 25 5 9 6.11 0.00 0 0.0 +dist.constr 26 5 10 8.79 0.00 0 0.0 +dist.constr 27 6 7 3.87 0.00 0 0.0 +dist.constr 28 6 8 5.61 0.00 0 0.0 +dist.constr 29 6 9 5.36 0.00 0 0.0 +dist.constr 30 6 10 6.73 0.00 0 0.0 +dist.constr 31 7 8 3.86 0.00 0 0.0 +dist.constr 32 7 9 5.70 0.00 0 0.0 +dist.constr 33 7 10 5.59 0.00 0 0.0 +dist.constr 34 8 9 3.88 0.00 0 0.0 +dist.constr 35 8 10 5.38 0.00 0 0.0 +dist.constr 36 9 10 3.86 0.00 0 0.0 Geometry of the virtual chain. Res d Theta Gamma Dsc Alpha Beta D 1 0.000 0.000 0.000 0.000 0.000 0.000 ASN 2 3.861 0.000 0.000 1.977 94.624 -178.093 LEU 3 3.876 92.239 0.000 2.195 102.878 -79.236 TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440 ILE 5 3.871 90.357 45.849 1.692 144.011 -104.516 GLN 6 3.846 89.090 55.194 2.338 170.986 -139.318 TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913 LEU 8 3.859 93.032 48.298 2.105 151.723 -105.899 LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960 ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646 GLY 11 3.891 89.908 56.679 0.000 0.000 0.000 GLY 12 3.864 100.181 -87.304 0.000 0.000 0.000 PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580 SER 14 3.876 89.537 4.261 1.267 144.515 -129.218 SER 15 3.875 91.815 66.108 1.262 161.047 -100.177 GLY 16 3.866 101.784 70.140 0.000 0.000 0.000 ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716 PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024 PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417 PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207 SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341 D 22 3.858 114.201 180.000 0.000 0.000 0.000 ******************************************************************************** Processor 0: end reading molecular data. ******************************************************************************** The following 36 distance constraints have been imposed 1 2 3 0 3.87640 0.00000 0.03702 2 2 4 0 5.57666 0.00000 0.02684 3 2 5 0 5.03889 0.00000 0.03009 4 2 6 0 6.31641 0.00000 0.02251 5 2 7 0 8.76681 0.00000 0.01075 6 2 8 0 9.90813 0.00000 0.00702 7 2 9 0 10.61482 0.00000 0.00525 8 2 10 0 12.89033 0.00000 0.00180 9 3 4 0 3.86050 0.00000 0.03711 10 3 5 0 5.48434 0.00000 0.02740 11 3 6 0 5.23878 0.00000 0.02888 12 3 7 0 6.42590 0.00000 0.02189 13 3 8 0 8.85122 0.00000 0.01043 14 3 9 0 10.21149 0.00000 0.00621 15 3 10 0 11.38863 0.00000 0.00374 16 4 5 0 3.87147 0.00000 0.03705 17 4 6 0 5.41330 0.00000 0.02783 18 4 7 0 4.90831 0.00000 0.03088 19 4 8 0 6.10832 0.00000 0.02371 20 4 9 0 8.64580 0.00000 0.01121 21 4 10 0 10.11108 0.00000 0.00647 22 5 6 0 3.84558 0.00000 0.03720 23 5 7 0 5.38909 0.00000 0.02797 24 5 8 0 5.07567 0.00000 0.02987 25 5 9 0 6.11071 0.00000 0.02369 26 5 10 0 8.79273 0.00000 0.01065 27 6 7 0 3.86660 0.00000 0.03708 28 6 8 0 5.60509 0.00000 0.02667 29 6 9 0 5.35795 0.00000 0.02816 30 6 10 0 6.72791 0.00000 0.02022 31 7 8 0 3.85852 0.00000 0.03712 32 7 9 0 5.69883 0.00000 0.02611 33 7 10 0 5.58812 0.00000 0.02678 34 8 9 0 3.88180 0.00000 0.03699 35 8 10 0 5.37698 0.00000 0.02804 36 9 10 0 3.86099 0.00000 0.03711 Replica exchange molecular dynamics (REMD) calculation. ******************************************************************************** Calling chainbuild Calling REMD MREMD 16 time before 5.078125000000000E-002 NREP= 16 i2rep 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 i2set 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 i,j,il,il1,i_index(i,j,il,il1) ifirst 1 nupa 1: 2 ndowna 1: nupa 2: 3 ndowna 2: 1 nupa 3: 4 ndowna 3: 2 nupa 4: 5 ndowna 4: 3 nupa 5: 6 ndowna 5: 4 nupa 6: 7 ndowna 6: 5 nupa 7: 8 ndowna 7: 6 nupa 8: 9 ndowna 8: 7 nupa 9: 10 ndowna 9: 8 nupa 10: 11 ndowna 10: 9 nupa 11: 12 ndowna 11: 10 nupa 12: 13 ndowna 12: 11 nupa 13: 14 ndowna 13: 12 nupa 14: 15 ndowna 14: 13 nupa 15: 16 ndowna 15: 14 nupa 16: ndowna 16: 15 REMD Temperature: 250.00000 ====================MD calculation start==================== Initial velocities randomly generated Initial velocities 0 0.02069 0.05735 -0.16550 0.00000 0.00000 0.00000 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 2 -0.32876 -0.20726 -0.00156 -0.06303 -0.02233 0.22619 3 0.25246 0.18847 0.12917 0.23917 0.13789 0.08528 4 0.09890 -0.10900 0.13430 0.09430 -0.08759 0.02991 5 0.05293 -0.08192 0.07599 0.03541 0.02418 -0.13426 6 0.01106 0.15012 -0.13429 -0.01486 0.10588 -0.15072 7 -0.00922 -0.05032 0.03343 -0.17306 0.05869 0.04136 8 -0.01642 0.12268 -0.04117 0.02116 0.09728 0.03398 9 -0.24153 -0.01761 0.08700 -0.20570 -0.15587 -0.04194 10 0.12837 -0.05524 -0.16763 0.18636 -0.14195 -0.15819 11 -0.12912 0.12012 -0.00669 0.00000 0.00000 0.00000 12 0.18024 -0.22147 0.01606 0.00000 0.00000 0.00000 13 -0.13972 0.25567 0.06619 0.05987 0.13532 0.09181 14 0.10136 -0.29158 0.14318 -0.02692 -0.08844 0.04927 15 0.13268 0.09441 -0.21684 -0.12710 0.07259 0.06988 16 -0.10926 0.13472 0.13695 0.00000 0.00000 0.00000 17 -0.08222 -0.14474 -0.18471 -0.07262 -0.07774 -0.09353 18 0.22036 0.08274 0.12819 -0.01893 0.09330 0.04480 19 -0.13103 -0.06596 -0.26603 -0.11327 -0.06258 -0.02718 20 0.26050 0.08237 0.51647 0.02143 0.14877 0.17591 21 0.00000 0.00000 0.00000 -0.12529 -0.05874 -0.20044 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 Calling the zero-angular momentum subroutine vcm right after adjustment: 2.021371575869251E-017 -1.735521049988750E-018 1.041312629993250E-017 alpha-carbon coordinates centroid coordinates X Y Z X Y Z D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ASN( 2) 3.86050 0.00000 0.00000 2.55159 1.47985 0.06557 LEU( 3) 4.01193 -3.87344 0.00000 3.96088 -4.50305 -2.10206 TYR( 4) 7.87243 -3.87344 0.00000 10.79652 -4.89021 -1.22632 ILE( 5) 7.89655 -1.17680 2.77774 7.76075 0.44675 2.31935 GLN( 6) 5.70141 -3.47509 4.94285 3.60888 -3.02771 5.88565 TRP( 7) 8.16996 -6.36206 4.22016 10.77228 -8.29798 2.61912 LEU( 8) 11.25658 -4.20989 5.07405 12.42370 -3.38205 3.52958 LYS( 9) 9.76612 -2.79308 8.36640 6.86736 -2.82804 9.12493 ASP( 10) 9.49962 -6.42561 9.64741 7.69328 -7.25489 9.53489 GLY( 11) 13.31647 -6.90493 9.06335 13.31647 -6.90493 9.06335 GLY( 12) 13.30671 -8.01769 5.36352 13.30671 -8.01769 5.36352 PRO( 13) 15.31165 -11.32992 5.02827 16.17763 -10.48298 4.32295 SER( 14) 15.75414 -11.41497 8.87760 16.77305 -10.71800 9.16233 SER( 15) 11.95328 -11.92981 9.42670 11.12717 -10.97987 9.51528 GLY( 16) 11.45094 -15.53878 8.13618 11.45094 -15.53878 8.13618 ARG( 17) 9.54906 -14.31220 5.00147 7.79760 -12.40573 7.22288 PRO( 18) 10.53690 -13.94710 1.26956 9.62009 -14.99504 1.15440 PRO( 19) 10.30439 -10.55356 -0.55592 11.52337 -10.99526 -1.06954 PRO( 20) 6.99735 -9.68439 -2.34313 7.03150 -8.66136 -1.39345 SER( 21) 7.20688 -9.78655 -6.20031 7.28380 -10.16020 -6.79638 D ( 22) 3.89984 -8.91739 -7.98752 3.89984 -8.91739 -7.98752 Geometry of the virtual chain. Res d Theta Gamma Dsc Alpha Beta D 1 0.000 0.000 0.000 0.000 0.000 0.000 ASN 2 3.861 0.000 0.000 1.977 94.624 -178.093 LEU 3 3.876 92.239 0.000 2.195 102.878 -79.236 TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440 ILE 5 3.871 90.357 45.849 1.692 144.011 -104.516 GLN 6 3.846 89.090 55.194 2.338 170.986 -139.318 TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913 LEU 8 3.859 93.032 48.298 2.105 151.723 -105.899 LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960 ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646 GLY 11 3.891 89.908 56.679 0.000 180.000 180.000 GLY 12 3.864 100.181 -87.304 0.000 180.000 180.000 PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580 SER 14 3.876 89.537 4.261 1.267 144.515 -129.218 SER 15 3.875 91.815 66.108 1.262 161.047 -100.177 GLY 16 3.866 101.784 70.140 0.000 180.000 180.000 ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716 PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024 PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417 PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207 SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341 D 22 3.858 114.201 180.000 0.000 180.000 180.000 Potential energy and its components Virtual-chain energies: EVDW= -1.798849E+01 WEIGHT= 1.000000D+00 (SC-SC) EVDW2= 4.471415E+01 WEIGHT= 1.233150D+00 (SC-p) EES= -9.165378E+01 WEIGHT= 9.459849D-01 (p-p) EVDWPP= -3.362882E+01 WEIGHT= 2.317300D-01 (p-p VDW) ESTR= 5.659036E+01 WEIGHT= 1.000000D+00 (stretching) EBE= -5.669935E+00 WEIGHT= 6.295400D-01 (bending) ESC= 1.734458E+02 WEIGHT= 1.055400D-01 (SC local) ETORS= 1.479510E+01 WEIGHT= 2.064020D+00 (torsional) ETORSD= 1.006444E+00 WEIGHT= 1.555350D+00 (double torsional) EHPB= 2.258117E-31 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) ECORR4= -6.528803E+01 WEIGHT= 2.541120D-01 (multi-body) ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) EELLO= -4.012900E+00 WEIGHT= 4.590562D-01 (electrostatic-local) ETURN3= 1.829789E+01 WEIGHT= 1.724339D+00 (turns, 3rd order) ETURN4= 6.580750E-01 WEIGHT= 8.554124D-01 (turns, 4th order) ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order) ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (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= 5.976608E+01 (total) Initial: Kinetic energy 2.56370E+01 potential energy 5.97661E+01 total energy 8.54031E+01 maximum acceleration 1.97137E+00 Setup time 5.468750000000000E-002 Velocities reset to random values, time 1999.80 Velocities reset to random values, time 3999.80 Velocities reset to random values, time 5999.80 Velocities reset to random values, time 7999.80 Velocities reset to random values, time 9999.80 Velocities reset to random values, time 11999.80 Velocities reset to random values, time 13999.80 Velocities reset to random values, time 15999.80 Velocities reset to random values, time 17999.80 Velocities reset to random values, time 19999.80 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= 40.8046875000000 3.906250000000000E-003 REMD writing rst time= 0.000000000000000E+000 REMD writing traj time= 3.906250000000000E-003 NREP 16 ACC 1 250.00000 0.00000 1 ACC 2 260.00000 1.00000 1 ACC 3 270.00000 1.00000 1 ACC 4 280.00000 0.00000 1 ACC 5 290.00000 0.00000 1 ACC 6 300.00000 1.00000 1 ACC 7 310.00000 0.00000 1 ACC 8 320.00000 1.00000 1 ACC 9 330.00000 1.00000 1 ACC 10 340.00000 1.00000 1 ACC 11 350.00000 0.00000 1 ACC 12 360.00000 1.00000 1 ACC 13 370.00000 0.00000 1 ACC 14 380.00000 1.00000 1 ACC 15 390.00000 1.00000 1 REMD scatter time= 0.000000000000000E+000 REMD exchange time= 7.812500000000000E-003 Velocities reset to random values, time 21999.80 Velocities reset to random values, time 23999.80 Velocities reset to random values, time 25999.80 Velocities reset to random values, time 27999.80 Velocities reset to random values, time 29999.80 Velocities reset to random values, time 31999.80 Velocities reset to random values, time 33999.80 Velocities reset to random values, time 35999.80 Velocities reset to random values, time 37999.80 Velocities reset to random values, time 39999.80 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= 81.6015625000000 0.000000000000000E+000 REMD writing rst time= 0.000000000000000E+000 REMD writing traj time= 3.906250000000000E-003 NREP 16 ACC 1 250.00000 0.00000 2 ACC 2 260.00000 0.50000 2 ACC 3 270.00000 1.00000 2 ACC 4 280.00000 0.50000 2 ACC 5 290.00000 0.50000 2 ACC 6 300.00000 1.00000 2 ACC 7 310.00000 0.00000 2 ACC 8 320.00000 0.50000 2 ACC 9 330.00000 1.00000 2 ACC 10 340.00000 1.00000 2 ACC 11 350.00000 0.00000 2 ACC 12 360.00000 1.00000 2 ACC 13 370.00000 0.50000 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 Velocities reset to random values, time 41999.80 Velocities reset to random values, time 43999.80 Velocities reset to random values, time 45999.80 Velocities reset to random values, time 47999.80 Velocities reset to random values, time 49999.80 Velocities reset to random values, time 51999.80 Velocities reset to random values, time 53999.80 Velocities reset to random values, time 55999.80 Velocities reset to random values, time 57999.80 Velocities reset to random values, time 59999.80 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= 122.531250000000 0.000000000000000E+000 REMD writing rst time= 3.906250000000000E-003 REMD writing traj time= 3.906250000000000E-003 NREP 16 ACC 1 250.00000 0.33333 3 ACC 2 260.00000 0.33333 3 ACC 3 270.00000 1.00000 3 ACC 4 280.00000 0.33333 3 ACC 5 290.00000 0.66667 3 ACC 6 300.00000 1.00000 3 ACC 7 310.00000 0.00000 3 ACC 8 320.00000 0.33333 3 ACC 9 330.00000 1.00000 3 ACC 10 340.00000 1.00000 3 ACC 11 350.00000 0.33333 3 ACC 12 360.00000 0.66667 3 ACC 13 370.00000 0.66667 3 ACC 14 380.00000 1.00000 3 ACC 15 390.00000 1.00000 3 REMD scatter time= 0.000000000000000E+000 REMD exchange time= 7.812500000000000E-003 Velocities reset to random values, time 61999.80 Velocities reset to random values, time 63999.80 Velocities reset to random values, time 65999.80 Velocities reset to random values, time 67999.80 Velocities reset to random values, time 69999.80 Velocities reset to random values, time 71999.80 Velocities reset to random values, time 73999.80 Velocities reset to random values, time 75999.80 Velocities reset to random values, time 77999.80 Velocities reset to random values, time 79999.80 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= 163.546875000000 0.000000000000000E+000 REMD writing rst time= 3.906250000000000E-003 REMD writing traj time= 0.000000000000000E+000 NREP 16 ACC 1 250.00000 0.50000 4 ACC 2 260.00000 0.25000 4 ACC 3 270.00000 0.75000 4 ACC 4 280.00000 0.25000 4 ACC 5 290.00000 0.75000 4 ACC 6 300.00000 0.75000 4 ACC 7 310.00000 0.00000 4 ACC 8 320.00000 0.50000 4 ACC 9 330.00000 1.00000 4 ACC 10 340.00000 1.00000 4 ACC 11 350.00000 0.50000 4 ACC 12 360.00000 0.75000 4 ACC 13 370.00000 0.50000 4 ACC 14 380.00000 1.00000 4 ACC 15 390.00000 1.00000 4 REMD scatter time= 0.000000000000000E+000 REMD exchange time= 3.906250000000000E-003 Velocities reset to random values, time 81999.80 Velocities reset to random values, time 83999.80 Velocities reset to random values, time 85999.80 Velocities reset to random values, time 87999.80 Velocities reset to random values, time 89999.80 Velocities reset to random values, time 91999.80 Velocities reset to random values, time 93999.80 Velocities reset to random values, time 95999.80 Velocities reset to random values, time 97999.80 Velocities reset to random values, time 99999.80 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= 204.277343750000 0.000000000000000E+000 REMD writing rst time= 0.000000000000000E+000 REMD writing traj time= 3.906250000000000E-003 NREP 16 ACC 1 250.00000 0.40000 5 ACC 2 260.00000 0.40000 5 ACC 3 270.00000 0.80000 5 ACC 4 280.00000 0.40000 5 ACC 5 290.00000 0.80000 5 ACC 6 300.00000 0.60000 5 ACC 7 310.00000 0.00000 5 ACC 8 320.00000 0.60000 5 ACC 9 330.00000 1.00000 5 ACC 10 340.00000 1.00000 5 ACC 11 350.00000 0.60000 5 ACC 12 360.00000 0.80000 5 ACC 13 370.00000 0.60000 5 ACC 14 380.00000 1.00000 5 ACC 15 390.00000 1.00000 5 REMD scatter time= 0.000000000000000E+000 REMD exchange time= 3.906250000000000E-003 Velocities reset to random values, time 101999.80 Velocities reset to random values, time 103999.80 Velocities reset to random values, time 105999.80 Velocities reset to random values, time 107999.80 Velocities reset to random values, time 109999.80 Velocities reset to random values, time 111999.80 Velocities reset to random values, time 113999.80 Velocities reset to random values, time 115999.80 Velocities reset to random values, time 117999.80 Velocities reset to random values, time 119999.80 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= 245.050781250000 0.000000000000000E+000 REMD writing rst time= 3.906250000000000E-003 REMD writing traj time= 3.906250000000000E-003 NREP 16 ACC 1 250.00000 0.33333 6 ACC 2 260.00000 0.50000 6 ACC 3 270.00000 0.66667 6 ACC 4 280.00000 0.50000 6 ACC 5 290.00000 0.83333 6 ACC 6 300.00000 0.50000 6 ACC 7 310.00000 0.00000 6 ACC 8 320.00000 0.66667 6 ACC 9 330.00000 1.00000 6 ACC 10 340.00000 0.83333 6 ACC 11 350.00000 0.50000 6 ACC 12 360.00000 0.83333 6 ACC 13 370.00000 0.66667 6 ACC 14 380.00000 1.00000 6 ACC 15 390.00000 1.00000 6 REMD scatter time= 0.000000000000000E+000 REMD exchange time= 7.812500000000000E-003 Velocities reset to random values, time 121999.80 Velocities reset to random values, time 123999.80 Velocities reset to random values, time 125999.80 Velocities reset to random values, time 127999.80 Velocities reset to random values, time 129999.80 Velocities reset to random values, time 131999.80 Velocities reset to random values, time 133999.80 Velocities reset to random values, time 135999.80 Velocities reset to random values, time 137999.80 Velocities reset to random values, time 139999.80 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= 287.152343750000 0.000000000000000E+000 REMD writing rst time= 0.000000000000000E+000 REMD writing traj time= 7.812500000000000E-003 NREP 16 ACC 1 250.00000 0.28571 7 ACC 2 260.00000 0.57143 7 ACC 3 270.00000 0.71429 7 ACC 4 280.00000 0.42857 7 ACC 5 290.00000 0.85714 7 ACC 6 300.00000 0.42857 7 ACC 7 310.00000 0.14286 7 ACC 8 320.00000 0.57143 7 ACC 9 330.00000 1.00000 7 ACC 10 340.00000 0.85714 7 ACC 11 350.00000 0.57143 7 ACC 12 360.00000 0.85714 7 ACC 13 370.00000 0.57143 7 ACC 14 380.00000 1.00000 7 ACC 15 390.00000 0.85714 7 REMD scatter time= 0.000000000000000E+000 REMD exchange time= 7.812500000000000E-003 Velocities reset to random values, time 141999.80 Velocities reset to random values, time 143999.80 Velocities reset to random values, time 145999.80 Velocities reset to random values, time 147999.80 Velocities reset to random values, time 149999.80 Velocities reset to random values, time 151999.80 Velocities reset to random values, time 153999.80 Velocities reset to random values, time 155999.80 Velocities reset to random values, time 157999.80 Velocities reset to random values, time 159999.80 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= 328.453125000000 0.000000000000000E+000 REMD writing rst time= 3.906250000000000E-003 REMD writing traj time= 3.906250000000000E-003 NREP 16 ACC 1 250.00000 0.25000 8 ACC 2 260.00000 0.50000 8 ACC 3 270.00000 0.62500 8 ACC 4 280.00000 0.37500 8 ACC 5 290.00000 0.87500 8 ACC 6 300.00000 0.37500 8 ACC 7 310.00000 0.12500 8 ACC 8 320.00000 0.62500 8 ACC 9 330.00000 1.00000 8 ACC 10 340.00000 0.87500 8 ACC 11 350.00000 0.50000 8 ACC 12 360.00000 0.87500 8 ACC 13 370.00000 0.62500 8 ACC 14 380.00000 0.87500 8 ACC 15 390.00000 0.87500 8 REMD scatter time= 0.000000000000000E+000 REMD exchange time= 7.812500000000000E-003 Velocities reset to random values, time 161999.80 Velocities reset to random values, time 163999.80 Velocities reset to random values, time 165999.80 Velocities reset to random values, time 167999.80 Velocities reset to random values, time 169999.80 Velocities reset to random values, time 171999.80 Velocities reset to random values, time 173999.80 Velocities reset to random values, time 175999.80 Velocities reset to random values, time 177999.80 Velocities reset to random values, time 179999.80 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= 369.187500000000 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 9 ACC 2 260.00000 0.44444 9 ACC 3 270.00000 0.66667 9 ACC 4 280.00000 0.33333 9 ACC 5 290.00000 0.88889 9 ACC 6 300.00000 0.44444 9 ACC 7 310.00000 0.11111 9 ACC 8 320.00000 0.55556 9 ACC 9 330.00000 1.00000 9 ACC 10 340.00000 0.88889 9 ACC 11 350.00000 0.44444 9 ACC 12 360.00000 0.88889 9 ACC 13 370.00000 0.55556 9 ACC 14 380.00000 0.88889 9 ACC 15 390.00000 0.88889 9 REMD scatter time= 0.000000000000000E+000 REMD exchange time= 3.906250000000000E-003 Velocities reset to random values, time 181999.80 Velocities reset to random values, time 183999.80 Velocities reset to random values, time 185999.80 Velocities reset to random values, time 187999.80 Velocities reset to random values, time 189999.80 Velocities reset to random values, time 191999.80 Velocities reset to random values, time 193999.80 Velocities reset to random values, time 195999.80 Velocities reset to random values, time 197999.80 Velocities reset to random values, time 199999.80 REMD synchro at 1000000 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 MIN ii_write= 1 writing restart at the end of run =================================== Timing =================================== MD calculations setup: 3.90625E-03 Energy & gradient evaluation: 3.76590E+02 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 MD steps: 4.10020E+02 ============================ End of MD calculation =========================== CG processor 0 is finishing work. Total wall clock time 410.074218750000 sec