-------------------------------------------------------------------------------- FILE ASSIGNMENT -------------------------------------------------------------------------------- Input file : 1lq7.inp Output file : 1lq7.out_GB Sidechain potential file : ../../PARAM/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_gap8g-sc SCp potential file : ../../PARAM/scp.parm Electrostatic potential file : ../../PARAM/electr_631Gdp.parm Cumulant coefficient file : ../../PARAM/fourier_opt.parm.1igd_hc_iter3_3 Torsional parameter file : ../../PARAM/torsion_631Gdp.parm Double torsional parameter file : ../../PARAM/torsion_double_631Gdp.parm Bond & inertia constant file : ../../PARAM/bond.parm Bending parameter file : ../../PARAM/thetaml.5parm Rotamer parameter file : ../../PARAM/scgauss.parm Threading database : ../../PARAM/patterns.cart -------------------------------------------------------------------------------- ******************************************************************************** United-residue force field calculation - serial job. ******************************************************************************** ### LAST MODIFIED 6/23/05 7:29PM by czarek ++++ Compile info ++++ Version 2.3 build 2522 compiled Wed Feb 7 10:22:35 2007 compiled by adam@matrix OS name: Linux OS release: 2.4.20-28.7smp OS version: #1 SMP Thu Dec 18 11:18:31 EST 2003 flags: FC= mpif90 OPT = -fast -pc 64 -tp p6 \ -Minline=name:scalar2,scalar,transpose2,matvec2... OPT1 = -C -g -fast -pc 64 -tp p6 FFLAGS = -c ${OPT} FFLAGS1 = -c ${OPT1} BIN = ../bin/unres_MD_Tc-pgf90.exe LIBS = -L../xdrf -lxdrf CPPFLAGS = -DLINUX -DUNRES -DMP -DMPI -DPGI -DS... ARCH = LINUX PP = /lib/cpp -P objectCSA = unres_CSA.o arcos.o cartprint.o cha... ++++ 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 Random seed: -3059743. -3059743 ran_num 0.9302273140895307 RMSDBC = 3.0 RMSDBC1 = 0.5 RMSDBC1MAX = 1.5 DRMS = 0.1 RMSDBCM = 3.0 Time limit (min): 60.0 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: 10000 Initial time step of numerical integration: 0.10000 natural units 4.89000 fs Maximum acceleration threshold to scale down the time step: 4.00000 Maximum predicted energy drift to reduce the timestep: 10.00000 Maximum velocity threshold to reduce velocities: 20.00000 Frequency of property output: 100 Frequency of coordinate output: 1000 Berendsen bath calculation Temperature: 300.00000 Coupling constant (tau): 1.00000 Momenta will be reset at zero every 1000 steps ============================== End of MD run setup ============================= Energy-term weights (unscaled): WSCC= 1.709050 (SC-SC) WSCP= 2.183100 (SC-p) WELEC= 1.066840 (p-p electr) WVDWPP= 0.270440 (p-p VDW) WBOND= 1.000000 (stretching) WANG= 1.175360 (bending) WSCLOC= 0.220700 (SC local) WTOR= 2.657980 (torsional) WTORD= 2.006460 (double torsional) WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) WEL_LOC= 0.427890 (multi-body 3-rd order) WCORR4= 0.235410 (multi-body 4th order) WCORR5= 0.000000 (multi-body 5th order) WCORR6= 0.000000 (multi-body 6th order) WTURN3= 1.681260 (turns, 3rd order) WTURN4= 0.750800 (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= 1.709050 (SC-SC) WSCP= 2.183100 (SC-p) WELEC= 1.066840 (p-p electr) WVDWPP= 0.270440 (p-p VDW) WBOND= 1.000000 (stretching) WANG= 1.175360 (bending) WSCLOC= 0.220700 (SC local) WTOR= 2.657980 (torsional) WTORD= 2.006460 (double torsional) WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) WEL_LOC= 0.427890 (multi-body 3-rd order) WCORR4= 0.235410 (multi-body 4th order) WCORR5= 0.000000 (multi-body 5th order) WCORR6= 0.000000 (multi-body 6th order) WTURN3= 1.681260 (turns, 3rd order) WTURN4= 0.750800 (turns, 4th order) WTURN6= 0.000000 (turns, 6th order) Reference temperature for weights calculation: 300.0000000000000 Parameters of the SS-bond potential: D0CM 3.780000000000000 AKCM 15.10000000000000 AKTH 11.00000000000000 AKCT 12.00000000000000 V1SS -1.080000000000000 V2SS 7.610000000000000 V3SS 13.70000000000000 EBR -5.500000000000000 PDB data will be read from file 1lq7.pdb 1 10 GLY -8.202 -15.036 -3.535 2 12 SER -5.756 -12.694 -5.224 3 18 ARG -5.747 -9.983 -2.583 4 6 VAL -3.156 -8.094 -4.594 5 19 LYS -6.011 -7.405 -6.981 6 9 ALA -8.198 -5.679 -4.419 7 5 LEU -4.933 -4.076 -3.371 8 15 GLU -3.823 -2.772 -6.748 9 15 GLU -6.783 -0.461 -6.269 10 19 LYS -5.661 0.889 -2.915 11 6 VAL -2.044 1.098 -4.011 12 19 LYS -3.004 2.831 -7.236 13 9 ALA -4.915 5.197 -4.984 14 5 LEU -1.916 5.462 -2.690 15 15 GLU 0.021 6.500 -5.773 16 15 GLU -1.962 9.436 -7.103 17 19 LYS -2.668 10.626 -3.580 18 6 VAL 0.771 10.106 -2.088 19 19 LYS 2.036 11.865 -5.191 20 9 ALA -0.745 14.427 -5.026 21 5 LEU 0.489 15.375 -1.575 22 10 GLY 2.488 18.560 -2.002 23 10 GLY 5.232 16.484 -0.427 24 10 GLY 8.481 17.952 0.843 25 10 GLY 8.902 15.964 4.036 26 18 ARG 5.810 14.005 5.001 27 4 ILE 5.136 11.529 2.219 28 15 GLU 8.682 10.217 2.041 29 15 GLU 8.039 8.100 5.112 30 5 LEU 4.758 6.589 3.979 31 19 LYS 6.298 6.555 0.522 32 19 LYS 9.057 4.423 1.995 33 19 LYS 6.737 1.749 3.337 34 7 TRP 4.597 2.250 0.255 35 15 GLU 7.687 1.056 -1.577 36 15 GLU 8.084 -1.981 0.647 37 5 LEU 4.338 -2.519 0.595 38 19 LYS 3.766 -2.464 -3.146 39 19 LYS 6.675 -4.878 -3.329 40 19 LYS 4.708 -7.100 -0.979 41 4 ILE 1.506 -6.910 -2.989 42 15 GLU 3.681 -8.195 -5.807 43 15 GLU 4.922 -11.365 -4.152 44 5 LEU 1.423 -11.691 -2.747 45 10 GLY 0.909 -15.357 -3.540 46 10 GLY 3.203 -17.845 -1.848 47 10 GLY 1.644 -17.131 1.526 48 10 GLY -1.599 -15.646 2.793 49 15 GLU 0.309 -13.118 4.864 50 6 VAL -1.486 -10.307 3.074 51 19 LYS -2.537 -9.161 6.525 52 19 LYS 0.805 -7.395 6.335 53 6 VAL 0.280 -5.707 2.988 54 15 GLU -3.134 -4.380 3.944 55 15 GLU -1.979 -3.130 7.324 56 15 GLU 0.812 -1.550 5.314 57 6 VAL -1.578 0.130 2.908 58 19 LYS -3.463 1.283 5.981 59 19 LYS -0.587 3.105 7.635 60 5 LEU -0.837 5.201 4.493 61 15 GLU -4.549 5.919 4.315 62 15 GLU -4.418 6.878 7.974 63 15 GLU -1.436 9.178 7.596 64 4 ILE -2.377 10.304 4.107 65 19 LYS -5.844 11.023 5.445 66 19 LYS -4.093 13.130 8.056 67 5 LEU -1.690 14.592 5.524 Nres: 67 1 10 GLY -8.202 -15.036 -3.535 -8.202 -15.036 -3.535 2 12 SER -5.756 -12.694 -5.224 -5.823 -12.486 -6.482 3 18 ARG -5.747 -9.983 -2.583 -6.547 -12.158 0.219 4 6 VAL -3.156 -8.094 -4.594 -2.204 -8.664 -5.544 5 19 LYS -6.011 -7.405 -6.981 -7.559 -7.494 -9.254 6 9 ALA -8.198 -5.679 -4.419 -8.597 -6.043 -3.877 7 5 LEU -4.933 -4.076 -3.371 -4.114 -4.625 -1.777 8 15 GLU -3.823 -2.772 -6.748 -4.095 -2.889 -9.387 9 15 GLU -6.783 -0.461 -6.269 -8.761 0.596 -6.147 10 19 LYS -5.661 0.889 -2.915 -6.689 0.819 -0.448 11 6 VAL -2.044 1.098 -4.011 -1.093 0.001 -4.169 12 19 LYS -3.004 2.831 -7.236 -3.873 3.113 -9.896 13 9 ALA -4.915 5.197 -4.984 -5.544 4.995 -4.597 14 5 LEU -1.916 5.462 -2.690 -2.200 4.542 -0.918 15 15 GLU 0.021 6.500 -5.773 1.151 6.134 -7.975 16 15 GLU -1.962 9.436 -7.103 -4.048 10.344 -8.580 17 19 LYS -2.668 10.626 -3.580 -5.346 9.989 -2.114 18 6 VAL 0.771 10.106 -2.088 1.497 8.913 -1.660 19 19 LYS 2.036 11.865 -5.191 2.026 12.098 -7.838 20 9 ALA -0.745 14.427 -5.026 -1.489 14.255 -4.964 21 5 LEU 0.489 15.375 -1.575 0.016 13.736 -0.419 22 10 GLY 2.488 18.560 -2.002 2.488 18.560 -2.002 23 10 GLY 5.232 16.484 -0.427 5.232 16.484 -0.427 24 10 GLY 8.481 17.952 0.843 8.481 17.952 0.843 25 10 GLY 8.902 15.964 4.036 8.902 15.964 4.036 26 18 ARG 5.810 14.005 5.001 3.498 17.056 5.852 27 4 ILE 5.136 11.529 2.219 4.625 12.502 0.651 28 15 GLU 8.682 10.217 2.041 10.801 10.233 1.365 29 15 GLU 8.039 8.100 5.112 6.963 7.571 7.374 30 5 LEU 4.758 6.589 3.979 3.411 8.054 3.243 31 19 LYS 6.298 6.555 0.522 6.592 7.883 -1.784 32 19 LYS 9.057 4.423 1.995 11.401 5.557 2.644 33 19 LYS 6.737 1.749 3.337 7.039 1.350 6.047 34 7 TRP 4.597 2.250 0.255 3.310 3.456 -2.833 35 15 GLU 7.687 1.056 -1.577 9.435 1.439 -3.090 36 15 GLU 8.084 -1.981 0.647 9.874 -1.235 2.570 37 5 LEU 4.338 -2.519 0.595 2.426 -1.645 0.706 38 19 LYS 3.766 -2.464 -3.146 4.190 -0.833 -5.529 39 19 LYS 6.675 -4.878 -3.329 9.726 -5.272 -3.075 40 19 LYS 4.708 -7.100 -0.979 5.659 -6.383 1.888 41 4 ILE 1.506 -6.910 -2.989 0.341 -5.401 -2.786 42 15 GLU 3.681 -8.195 -5.807 4.890 -7.512 -7.814 43 15 GLU 4.922 -11.365 -4.152 7.232 -12.325 -3.099 44 5 LEU 1.423 -11.691 -2.747 0.247 -10.316 -1.732 45 10 GLY 0.909 -15.357 -3.540 0.909 -15.357 -3.540 46 10 GLY 3.203 -17.845 -1.848 3.203 -17.845 -1.848 47 10 GLY 1.644 -17.131 1.526 1.644 -17.131 1.526 48 10 GLY -1.599 -15.646 2.793 -1.599 -15.646 2.793 49 15 GLU 0.309 -13.118 4.864 2.642 -14.123 5.951 50 6 VAL -1.486 -10.307 3.074 -2.419 -10.381 1.953 51 19 LYS -2.537 -9.161 6.525 -4.203 -11.082 7.074 52 19 LYS 0.805 -7.395 6.335 3.296 -8.992 7.239 53 6 VAL 0.280 -5.707 2.988 0.109 -6.148 1.606 54 15 GLU -3.134 -4.380 3.944 -5.251 -5.694 3.338 55 15 GLU -1.979 -3.130 7.324 -1.511 -3.840 9.882 56 15 GLU 0.812 -1.550 5.314 2.800 -1.875 5.720 57 6 VAL -1.578 0.130 2.908 -2.083 -0.512 1.697 58 19 LYS -3.463 1.283 5.981 -5.586 -0.123 7.438 59 19 LYS -0.587 3.105 7.635 1.712 3.997 7.909 60 5 LEU -0.837 5.201 4.493 0.374 4.674 2.787 61 15 GLU -4.549 5.919 4.315 -6.399 4.810 2.982 62 15 GLU -4.418 6.878 7.974 -5.157 5.019 9.157 63 15 GLU -1.436 9.178 7.596 1.229 9.527 7.571 64 4 ILE -2.377 10.304 4.107 -2.051 9.346 2.487 65 19 LYS -5.844 11.023 5.445 -8.126 10.319 7.256 66 19 LYS -4.093 13.130 8.056 -2.925 13.297 10.885 67 5 LEU -1.690 14.592 5.524 0.009 13.524 4.817 68 21 D 0.061 16.699 8.135 0.061 16.699 8.135 nsup= 67 nstart_sup= 0 ITEL 1 10 1 2 12 1 3 18 1 4 6 1 5 19 1 6 9 1 7 5 1 8 15 1 9 15 1 10 19 1 11 6 1 12 19 1 13 9 1 14 5 1 15 15 1 16 15 1 17 19 1 18 6 1 19 19 1 20 9 1 21 5 1 22 10 1 23 10 1 24 10 1 25 10 1 26 18 1 27 4 1 28 15 1 29 15 1 30 5 1 31 19 1 32 19 1 33 19 1 34 7 1 35 15 1 36 15 1 37 5 1 38 19 1 39 19 1 40 19 1 41 4 1 42 15 1 43 15 1 44 5 1 45 10 1 46 10 1 47 10 1 48 10 1 49 15 1 50 6 1 51 19 1 52 19 1 53 6 1 54 15 1 55 15 1 56 15 1 57 6 1 58 19 1 59 19 1 60 5 1 61 15 1 62 15 1 63 15 1 64 4 1 65 19 1 66 19 1 67 5 0 ns= 0 iss: Boundaries in phi angle sampling: GLY 1 -180.0 180.0 SER 2 -180.0 180.0 ARG 3 -180.0 180.0 VAL 4 -180.0 180.0 LYS 5 -180.0 180.0 ALA 6 -180.0 180.0 LEU 7 -180.0 180.0 GLU 8 -180.0 180.0 GLU 9 -180.0 180.0 LYS 10 -180.0 180.0 VAL 11 -180.0 180.0 LYS 12 -180.0 180.0 ALA 13 -180.0 180.0 LEU 14 -180.0 180.0 GLU 15 -180.0 180.0 GLU 16 -180.0 180.0 LYS 17 -180.0 180.0 VAL 18 -180.0 180.0 LYS 19 -180.0 180.0 ALA 20 -180.0 180.0 LEU 21 -180.0 180.0 GLY 22 -180.0 180.0 GLY 23 -180.0 180.0 GLY 24 -180.0 180.0 GLY 25 -180.0 180.0 ARG 26 -180.0 180.0 ILE 27 -180.0 180.0 GLU 28 -180.0 180.0 GLU 29 -180.0 180.0 LEU 30 -180.0 180.0 LYS 31 -180.0 180.0 LYS 32 -180.0 180.0 LYS 33 -180.0 180.0 TRP 34 -180.0 180.0 GLU 35 -180.0 180.0 GLU 36 -180.0 180.0 LEU 37 -180.0 180.0 LYS 38 -180.0 180.0 LYS 39 -180.0 180.0 LYS 40 -180.0 180.0 ILE 41 -180.0 180.0 GLU 42 -180.0 180.0 GLU 43 -180.0 180.0 LEU 44 -180.0 180.0 GLY 45 -180.0 180.0 GLY 46 -180.0 180.0 GLY 47 -180.0 180.0 GLY 48 -180.0 180.0 GLU 49 -180.0 180.0 VAL 50 -180.0 180.0 LYS 51 -180.0 180.0 LYS 52 -180.0 180.0 VAL 53 -180.0 180.0 GLU 54 -180.0 180.0 GLU 55 -180.0 180.0 GLU 56 -180.0 180.0 VAL 57 -180.0 180.0 LYS 58 -180.0 180.0 LYS 59 -180.0 180.0 LEU 60 -180.0 180.0 GLU 61 -180.0 180.0 GLU 62 -180.0 180.0 GLU 63 -180.0 180.0 ILE 64 -180.0 180.0 LYS 65 -180.0 180.0 LYS 66 -180.0 180.0 LEU 67 -180.0 180.0 D 68 -180.0 180.0 nsup= 67 nsup= 67 nstart_sup= 1 nstart_seq= 1 NZ_START= 1 NZ_END= 67 IZ_SC= 0 Contact order: 0.3193590869183494 Shifting contacts: 1 1 1 LEU 7 VAL 4 2 VAL 11 LEU 7 3 LEU 14 LYS 10 4 LEU 14 VAL 11 5 VAL 18 LEU 14 6 LEU 21 VAL 18 7 ILE 27 VAL 18 8 ILE 27 LEU 21 9 ILE 27 GLY 23 10 LEU 30 VAL 18 11 LEU 30 ILE 27 12 LYS 31 VAL 18 13 LYS 31 ILE 27 14 LYS 32 GLU 28 15 TRP 34 VAL 11 16 TRP 34 LEU 14 17 TRP 34 VAL 18 18 GLU 36 LYS 33 19 LEU 37 VAL 11 20 LYS 38 VAL 11 21 LYS 38 TRP 34 22 LYS 40 LEU 37 23 ILE 41 VAL 4 24 ILE 41 LEU 7 25 ILE 41 VAL 11 26 ILE 41 LEU 37 27 LEU 44 VAL 4 28 LEU 44 ILE 41 29 VAL 50 ARG 3 30 VAL 50 LEU 44 31 LYS 52 GLU 49 32 VAL 53 LEU 7 33 VAL 53 LEU 37 34 VAL 53 LYS 40 35 VAL 53 ILE 41 36 VAL 53 LEU 44 37 VAL 53 VAL 50 38 GLU 54 LEU 7 39 GLU 54 VAL 50 40 GLU 56 LYS 33 41 GLU 56 LEU 37 42 VAL 57 LEU 7 43 VAL 57 LYS 10 44 VAL 57 VAL 11 45 VAL 57 LEU 14 46 VAL 57 LEU 37 47 VAL 57 VAL 53 48 LEU 60 LEU 14 49 LEU 60 VAL 18 50 LEU 60 LEU 30 51 LEU 60 VAL 57 52 GLU 61 LYS 10 53 GLU 61 LEU 14 54 GLU 62 LYS 58 55 GLU 63 LEU 30 56 ILE 64 LEU 14 57 ILE 64 LYS 17 58 ILE 64 VAL 18 59 ILE 64 LEU 21 60 ILE 64 LEU 30 61 ILE 64 LEU 60 62 LEU 67 LEU 21 63 LEU 67 ARG 26 64 LEU 67 ILE 27 65 LEU 67 LEU 30 66 LEU 67 GLU 63 67 LEU 67 ILE 64 Geometry of the virtual chain. Res d Theta Phi Dsc Alpha Omega GLY 1 0.000 0.000 0.000 0.000 0.000 0.000 SER 2 3.784 0.000 0.000 1.276 144.939 -94.284 ARG 3 3.785 97.666 0.000 3.636 132.847 -136.663 VAL 4 3.785 89.333 177.476 1.461 120.485 -67.491 LYS 5 3.785 84.811 71.708 2.751 151.871 -7.605 ALA 6 3.785 95.278 58.423 0.765 132.978 -83.541 LEU 7 3.785 83.231 41.781 1.874 159.456 -117.163 GLU 8 3.786 98.730 52.453 2.655 127.393 -42.771 GLU 9 3.786 82.425 68.389 2.246 139.933 -10.602 LYS 10 3.786 95.627 54.877 2.673 164.411 -81.368 VAL 11 3.785 92.658 40.616 1.461 137.613 -78.366 LYS 12 3.785 91.698 47.994 2.812 149.544 -30.888 ALA 13 3.784 84.681 51.646 0.765 130.308 -80.013 LEU 14 3.785 90.248 46.537 2.017 152.909 -147.404 GLU 15 3.786 86.046 55.069 2.502 139.867 -30.986 GLU 16 3.784 103.344 54.915 2.712 142.391 -46.710 LYS 17 3.785 90.833 37.628 3.118 147.778 -92.352 VAL 18 3.785 98.873 42.913 1.460 140.342 -74.863 LYS 19 3.785 85.218 47.394 2.658 127.030 -40.335 ALA 20 3.785 91.907 41.951 0.766 126.974 -76.135 LEU 21 3.786 88.266 58.560 2.061 155.447 -157.937 GLY 22 3.785 106.265 101.124 0.000 0.000 0.000 GLY 23 3.784 82.782 -122.635 0.000 0.000 0.000 GLY 24 3.785 123.323 -168.063 0.000 0.000 0.000 GLY 25 3.785 100.070 139.318 0.000 0.000 0.000 ARG 26 3.785 113.331 -11.596 3.921 126.029 -109.245 ILE 27 3.785 107.256 61.845 1.915 121.565 -93.204 GLU 28 3.785 95.422 48.830 2.224 158.348 -19.209 GLU 29 3.785 89.803 78.416 2.560 123.110 -30.298 LEU 30 3.786 97.334 48.356 2.122 102.856 -71.033 LYS 31 3.785 85.659 36.445 2.678 159.703 -52.243 LYS 32 3.785 86.916 58.012 2.683 156.818 -116.068 LYS 33 3.786 95.112 55.594 2.756 151.563 -138.866 TRP 34 3.785 87.957 36.487 3.556 129.060 -19.927 GLU 35 3.785 83.732 62.879 2.344 161.223 -20.594 GLU 36 3.785 93.115 50.005 2.731 132.834 -114.702 LEU 37 3.785 90.124 40.742 2.105 125.264 -41.593 LYS 38 3.785 99.270 51.927 2.919 132.849 -53.798 LYS 39 3.785 85.547 48.115 3.086 147.472 -52.556 LYS 40 3.785 86.846 56.607 3.105 138.553 -118.164 ILE 41 3.785 94.614 49.064 1.917 143.243 -104.324 GLU 42 3.785 83.812 56.085 2.440 160.828 -41.860 GLU 43 3.785 98.465 56.994 2.714 158.179 -74.861 LEU 44 3.785 86.063 38.858 2.074 176.659 102.329 GLY 45 3.786 97.537 133.746 0.000 0.000 0.000 GLY 46 3.784 117.437 63.081 0.000 0.000 0.000 GLY 47 3.785 91.425 68.516 0.000 0.000 0.000 GLY 48 3.785 136.496 20.218 0.000 0.000 0.000 GLU 49 3.784 90.762 -125.179 2.763 152.424 -134.490 VAL 50 3.785 89.897 122.644 1.460 142.703 -83.682 LYS 51 3.785 85.720 124.240 2.601 134.737 -146.671 LYS 52 3.785 81.391 86.531 3.094 143.151 -99.233 VAL 53 3.785 97.470 51.282 1.461 134.249 -62.621 GLU 54 3.786 93.331 48.720 2.564 146.346 -99.045 GLU 55 3.784 93.790 46.265 2.696 150.633 -59.911 GLU 56 3.785 83.606 49.391 2.055 169.300 -167.852 VAL 57 3.785 93.281 52.240 1.460 144.237 -96.089 LYS 58 3.785 86.192 47.933 2.934 153.109 -85.425 LYS 59 3.785 97.066 57.243 2.481 125.481 -24.034 LEU 60 3.785 81.584 62.431 2.157 146.082 -95.013 GLU 61 3.785 102.055 48.277 2.536 154.995 -88.741 GLU 62 3.785 88.204 47.695 2.324 141.973 -124.114 GLU 63 3.785 94.858 49.253 2.688 141.300 -43.881 ILE 64 3.785 94.414 33.242 1.910 142.265 -87.362 LYS 65 3.785 87.615 50.150 2.997 129.513 -40.349 LYS 66 3.785 85.747 53.802 3.065 150.194 -47.165 LEU 67 3.785 92.709 41.921 2.128 119.269 71.699 D 68 3.785 92.709 180.000 0.000 0.000 0.000 MD calculation. ******************************************************************************** MODECALC 12 Calling hpb_partition Calling chainbuild Calling MD ====================MD calculation start==================== Initial velocities randomly generated Initial backbone velocities 1.4324862923909696E-002 2.3060954008253298E-002 -6.3792993845931081E-002 -8.2464915343916019E-002 -0.2516070235700686 4.4210010401026594E-002 0.2349723051592712 0.2200841538295040 4.5251610843760908E-002 -0.2124003419082547 9.9285486849185425E-002 0.2048035611662629 7.7626734156010748E-002 -8.7230774321129179E-004 -0.1852910092927067 -0.2054954346205523 -0.1736398459036022 -0.1193947039305000 0.1245242224603375 6.3589487597254690E-002 0.1871120037722356 0.1085692605935111 -0.1211347283374747 0.1589635466612328 -4.1993868126625458E-002 0.1494245316364686 -0.1751136041361389 4.5499187413129132E-002 0.1391643290712960 -7.4924978376189770E-002 -0.1007527144082593 -9.4770335703041155E-002 0.1192507570729570 1.0302646343144954E-002 -0.1824544980594764 1.8806866372040909E-002 2.0920028362883287E-002 0.1805078120910424 -5.5851440541906729E-002 9.6207778982298642E-002 -0.1173909006237467 -4.5240357604825476E-002 -0.1736090004471858 0.1442184294965889 0.1982043058289817 0.1365034893907223 -0.2585507088530808 -0.3188849711363511 3.8504939006249179E-002 0.3885919699737705 0.2140040568464722 -0.1996533930470889 -0.3021906086559044 -0.1429297339109604 0.2830864519465333 0.1942072909175117 0.1668972686226336 -2.5009110398121850E-002 -0.1539663305831705 3.3125498973123864E-002 -0.2653534518187957 6.1246273825734745E-003 -0.2663425789513554 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5.3788648985821466E-002 -0.2318059904911159 -2.4765346405761060E-002 3.1546153241568797E-002 0.2036388793504332 0.2035443175573332 4.8880784251840064E-002 -9.1849026940734912E-002 -0.2640105127434449 -0.1664864397727329 -0.1644399360070172 0.2714500887463680 0.1254803538812205 0.2905681902197779 -0.2677371159394383 -8.0014734334484388E-002 7.9170110496708981E-002 -5.4238640366009294E-002 0.1280872346094246 -0.4081061838591050 0.2956054696767141 -0.1235050569467009 0.2559044578781554 -0.2070043511404440 0.3624319212495557 0.1812129646683664 0.2023685570588290 -0.4691434326433293 -0.1297979531903272 -0.1350928301820909 0.1945932776131060 1.4914424954272758E-002 7.7448936624335785E-002 -1.3755367963486167E-002 0.1057457714064048 0.1888182761468886 -0.2079280387445719 -0.2504600248204472 -0.2891337828028493 0.1804651015531500 0.2493889640084464 9.4962876224487598E-002 -0.1539821604243660 -0.2014391684545395 1.3572701889875609E-002 Initial side-chain velocities 0.0000000000000000 0.0000000000000000 0.0000000000000000 -0.1128976735269540 -0.1965949792386982 0.2211441217084325 3.0840424159487507E-002 0.2281020550113027 0.1238616378424910 -3.1040253760719612E-002 -0.1501844388511035 3.8672254960298460E-002 4.8246430378742033E-003 -0.1015911880843303 -0.1040537234213796 0.1772133216510695 -8.2857931766127972E-002 7.4564862035412709E-002 -5.3140401556500354E-003 7.8579529839689730E-002 0.3066032664047404 2.1471828522848875E-002 5.3502638228185599E-003 -4.1247651069860218E-002 -0.1971600402464241 -1.9954576732187446E-002 -9.3622111683778808E-002 -0.1240074247131901 -8.7658046078999625E-002 2.3115291660446142E-002 6.3929983382066791E-002 -0.1761331732204543 -2.4122050369819807E-002 3.9066335309932789E-002 -6.5708451172283464E-003 -1.9752318162502769E-003 -0.1872309227414096 9.6209937168067743E-002 -0.2987487502193678 -6.4872837326460777E-002 -0.1522866020207292 -2.7497036638504957E-002 -9.4802064151263021E-002 6.1872894468107962E-002 0.1027506447796682 6.4531225453570507E-003 -4.9885412379387128E-002 -0.1550494987688242 -2.2513286095570235E-002 0.1148300140079759 0.1464987194810843 -0.1474138469234483 -0.1104214711490018 9.2516503944193058E-002 0.1604253882373028 0.1003029138674276 3.3910225144852730E-002 -0.1480451857506935 -0.2378844165105173 3.5090183973688394E-002 -0.2440578360316706 8.8335333812237522E-002 -2.5691870356172615E-002 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 -4.1691606533965651E-002 0.1820899617638935 -0.1547176386442052 9.1566092684170872E-002 2.8981350251546560E-002 -9.0136233570203892E-002 5.8503395041750199E-002 -1.2899282930997089E-002 0.1023277278845082 -1.4266343423712360E-002 0.1530244339164073 0.1318802229635456 -0.1649931724100239 -0.2433842458246506 9.2231934180517801E-002 0.1166768375589941 -0.1302673672831547 9.1487215849938970E-002 9.0856949488808709E-003 -0.1052101603064049 -2.7281596920403173E-003 6.8220369646984436E-003 9.3747825697828109E-002 -1.6355302908142386E-003 -1.0534363894661591E-002 -1.0819613667425065E-002 -9.6410871012427855E-002 -0.1039749136265033 3.6199636814580738E-002 -1.6460015453868191E-002 -0.1319310491862090 5.8724270593085750E-002 0.1192202875752651 0.1007618987639446 1.9336570278769926E-003 -3.4142489774448497E-002 0.1162438828399469 9.0538895467218357E-002 6.6254369783463005E-002 -0.1018561820556906 -0.2111554657171823 -6.0460853031793889E-002 -0.1506674375211980 -0.1204734189820305 -9.0545767572239484E-003 1.1614897982892078E-003 5.1554037897888332E-002 -5.2907901984905257E-002 -1.8333084465663507E-003 -6.2459150645534569E-002 -0.1284673786598817 8.8120568813547013E-002 2.3247913917364142E-002 -0.2760670594013803 7.7578377221085937E-002 -7.7807224412136042E-002 -1.0306570558009995E-002 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 3.7306513760719140E-003 0.2830265456103908 0.1479120392363028 0.1853307997081223 0.1635165519528208 -0.3517909332220863 1.4051459178707981E-002 4.3512471795343117E-002 6.0872311857795349E-004 1.2868148363352661E-002 -3.2281503343216942E-002 6.6542301536674309E-002 7.4176333239815264E-002 2.2515981030951098E-002 -1.8694740029181549E-002 -0.1225191232346091 -0.1032499261762106 4.4129444585356072E-002 -6.0095842877336345E-002 2.3636181620223597E-002 9.7312033439731334E-002 4.5591139018909743E-002 0.2353208404783136 -0.1965741124709957 -9.7003323149892005E-002 -0.1041592116719632 0.1707224339787879 1.7728960574588033E-002 -0.1225938955576677 0.1890948450611761 -9.7917828477334865E-002 0.2573138955404320 -6.9142137648953961E-002 1.1305196229803758E-002 2.7361458839471791E-002 0.1876208252212528 -0.1811543402677132 -4.2039185431163038E-002 -0.1421901131548191 7.4421998096865760E-002 -1.6472472460452674E-002 0.1137278111643500 -9.7160397210836553E-002 -5.8307027338373141E-002 -8.7150987686124655E-002 3.7773615249674375E-002 -0.1662975819391843 -0.1860983042430830 0.3317992931711260 -5.0067177269952552E-002 -1.7276023488628245E-002 0.1506033179782202 -0.1396242439187054 -9.6047876411386000E-002 5.7642615805661883E-002 5.0647958430279676E-002 -5.4442329630573374E-002 Calling the zero-angular momentum subroutine vcm right after adjustment: 3.8017267830930992E-018 3.7512350992551431E-017 3.1965691017999598E-017 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 SER( 2) 3.78426 0.00000 0.00000 4.43080 0.82260 0.73120 ARG( 3) 4.28912 -3.75095 0.00000 1.17596 -4.56902 -1.69032 VAL( 4) 8.03046 -3.20295 -0.16665 8.71726 -2.03177 -0.70567 LYS( 5) 7.67688 -2.06100 3.42423 7.63590 -0.39832 5.61546 ALA( 6) 6.18799 -5.30750 4.67698 5.46322 -5.52299 4.56134 LEU( 7) 8.82268 -6.85717 2.44425 8.30071 -7.65506 0.83086 GLU( 8) 11.85440 -5.01653 3.76993 12.78377 -2.94825 5.15151 GLU( 9) 11.15761 -7.11075 6.84573 10.47899 -8.04696 8.77080 LYS( 10) 11.22135 -10.44209 5.04884 9.41268 -12.36911 4.64720 VAL( 11) 14.17775 -9.43223 2.91169 14.18390 -8.52940 1.76357 LYS( 12) 16.06915 -8.15719 5.93202 16.86946 -6.37844 7.95788 ALA( 13) 15.29311 -11.55269 7.41177 14.58882 -11.77210 7.61579 LEU( 14) 16.37169 -13.22143 4.19018 14.82802 -14.01166 3.16079 GLU( 15) 19.64210 -11.36540 4.63048 21.12868 -9.35274 4.63264 GLU( 16) 20.77100 -12.39425 8.09289 20.64392 -12.02303 10.77656 LYS( 17) 19.47874 -15.90707 7.53054 16.69929 -16.84643 8.58747 VAL( 18) 20.71385 -16.42375 3.99066 20.25391 -15.92687 2.69702 LYS( 19) 24.00505 -15.07034 5.27876 25.32372 -13.19691 6.62558 ALA( 20) 23.71944 -17.06997 8.47954 23.10453 -17.07064 8.93579 LEU( 21) 23.56349 -20.20890 6.36917 21.72754 -20.08478 5.44187 GLY( 22) 27.01728 -21.75015 6.50501 27.01728 -21.75015 6.50501 GLY( 23) 26.80315 -21.39406 2.74372 26.80315 -21.39406 2.74372 GLY( 24) 29.24486 -23.02840 0.35816 29.24486 -23.02840 0.35816 GLY( 25) 26.86154 -24.16153 -2.35485 26.86154 -24.16153 -2.35485 ARG( 26) 23.21990 -23.90783 -1.35311 23.23427 -26.70438 1.39581 ILE( 27) 22.49358 -20.25567 -0.67596 23.46555 -19.72284 0.88527 GLU( 28) 24.05305 -18.98070 -3.88059 25.73426 -18.29546 -5.16547 GLU( 29) 20.95661 -20.02812 -5.78878 18.92408 -21.50966 -6.26736 LEU( 30) 18.40646 -18.47368 -3.46237 18.77058 -18.96191 -1.42967 LYS( 31) 20.92375 -15.67995 -3.03587 22.96491 -14.74211 -1.57849 LYS( 32) 20.73018 -15.20884 -6.78658 22.65712 -16.23130 -8.34856 LYS( 33) 16.97677 -14.72072 -6.87198 15.71556 -16.51030 -8.54531 TRP( 34) 17.27918 -12.86697 -3.58542 18.57215 -11.38701 -0.62121 GLU( 35) 19.35516 -10.44211 -5.62020 21.39750 -9.38283 -6.06652 GLU( 36) 16.73961 -10.16601 -8.34229 17.49995 -11.96145 -10.25497 LEU( 37) 14.00858 -10.09915 -5.72280 13.26441 -10.90414 -3.92609 LYS( 38) 15.34260 -7.32398 -3.52186 17.68958 -6.50947 -1.98989 LYS( 39) 15.81057 -5.39441 -6.74381 17.42532 -5.07894 -9.35494 LYS( 40) 12.11516 -5.93573 -7.36012 11.89380 -8.50464 -9.08945 ILE( 41) 11.06021 -4.79214 -3.90928 11.15078 -6.01058 -2.43172 GLU( 42) 12.92852 -1.63304 -4.83254 15.02804 -0.43388 -4.50309 GLU( 43) 11.03014 -0.76567 -7.99037 11.45913 -0.76128 -10.66997 LEU( 44) 7.93968 -1.92687 -6.13997 7.57759 -3.68108 -5.09351 GLY( 45) 5.69258 0.97986 -7.05322 5.69258 0.97986 -7.05322 GLY( 46) 4.88038 1.47192 -10.71568 4.88038 1.47192 -10.71568 GLY( 47) 2.80869 -1.69482 -10.77893 2.80869 -1.69482 -10.77893 GLY( 48) 1.06608 -3.88695 -8.23228 1.06608 -3.88695 -8.23228 GLU( 49) 2.93953 -6.92465 -9.49038 3.34039 -6.91563 -12.22399 VAL( 50) 4.31790 -7.50616 -6.01334 4.16953 -6.68130 -4.81745 LYS( 51) 2.80755 -10.96500 -6.30062 0.29724 -10.29715 -6.16950 LYS( 52) 6.14544 -11.66636 -7.94087 6.36396 -11.12483 -10.97951 VAL( 53) 8.34461 -10.23252 -5.21413 8.57856 -8.90902 -4.64191 GLU( 54) 6.53250 -12.10043 -2.46506 4.62177 -10.97604 -1.17678 GLU( 55) 6.54407 -15.38490 -4.34469 5.26559 -16.84589 -6.21499 GLU( 56) 10.22301 -14.62316 -4.80443 11.12609 -14.55747 -6.64892 VAL( 57) 10.79177 -14.06105 -1.10526 10.60859 -12.76802 -0.45154 LYS( 58) 8.91540 -17.30608 -0.58087 6.02291 -17.69997 -0.29064 LYS( 59) 11.16372 -19.49178 -2.70090 13.07946 -20.07683 -4.16430 LEU( 60) 13.70165 -18.45222 -0.09205 14.92000 -16.70965 -0.45665 GLU( 61) 11.82615 -19.08936 3.13328 10.53872 -17.51765 4.65129 GLU( 62) 10.87124 -22.48758 1.76750 8.71512 -22.26535 0.92859 GLU( 63) 14.39082 -23.41720 0.73138 16.34028 -23.39571 -1.11935 ILE( 64) 16.03667 -21.55066 3.58335 16.37728 -19.67258 3.65382 LYS( 65) 13.64353 -23.32618 5.91738 10.92453 -24.45260 6.48320 LYS( 66) 14.91394 -26.52060 4.33482 14.51007 -28.69022 2.20786 LEU( 67) 18.50204 -25.31733 4.35856 19.25535 -23.95034 2.91243 D ( 68) 19.77245 -28.51176 2.77600 19.77245 -28.51176 2.77600 Geometry of the virtual chain. Res d Theta Phi Dsc Alpha Omega GLY 1 0.000 0.000 0.000 0.000 0.000 0.000 SER 2 3.784 0.000 0.000 1.276 144.939 -94.284 ARG 3 3.785 97.666 0.000 3.636 132.847 -136.663 VAL 4 3.785 89.333 177.476 1.461 120.485 -67.491 LYS 5 3.785 84.811 71.708 2.751 151.871 -7.605 ALA 6 3.785 95.278 58.423 0.765 132.978 -83.541 LEU 7 3.785 83.231 41.781 1.874 159.456 -117.163 GLU 8 3.786 98.730 52.453 2.655 127.393 -42.771 GLU 9 3.786 82.425 68.389 2.246 139.933 -10.602 LYS 10 3.786 95.627 54.877 2.673 164.411 -81.368 VAL 11 3.785 92.658 40.616 1.461 137.613 -78.366 LYS 12 3.785 91.698 47.994 2.812 149.544 -30.888 ALA 13 3.784 84.681 51.646 0.765 130.308 -80.013 LEU 14 3.785 90.248 46.537 2.017 152.909 -147.404 GLU 15 3.786 86.046 55.069 2.502 139.867 -30.986 GLU 16 3.784 103.344 54.915 2.712 142.391 -46.710 LYS 17 3.785 90.833 37.628 3.118 147.778 -92.352 VAL 18 3.785 98.873 42.913 1.460 140.342 -74.863 LYS 19 3.785 85.218 47.394 2.658 127.030 -40.335 ALA 20 3.785 91.907 41.951 0.766 126.974 -76.135 LEU 21 3.786 88.266 58.560 2.061 155.447 -157.937 GLY 22 3.785 106.265 101.124 0.000 0.000 180.000 GLY 23 3.784 82.782 -122.635 0.000 0.000 180.000 GLY 24 3.785 123.323 -168.063 0.000 0.000 180.000 GLY 25 3.785 100.070 139.318 0.000 0.000 180.000 ARG 26 3.785 113.331 -11.596 3.921 126.029 -109.245 ILE 27 3.785 107.256 61.845 1.915 121.565 -93.204 GLU 28 3.785 95.422 48.830 2.224 158.348 -19.209 GLU 29 3.785 89.803 78.416 2.560 123.110 -30.298 LEU 30 3.786 97.334 48.356 2.122 102.856 -71.033 LYS 31 3.785 85.659 36.445 2.678 159.703 -52.243 LYS 32 3.785 86.916 58.012 2.683 156.818 -116.068 LYS 33 3.786 95.112 55.594 2.756 151.563 -138.866 TRP 34 3.785 87.957 36.487 3.556 129.060 -19.927 GLU 35 3.785 83.732 62.879 2.344 161.223 -20.594 GLU 36 3.785 93.115 50.005 2.731 132.834 -114.702 LEU 37 3.785 90.124 40.742 2.105 125.264 -41.593 LYS 38 3.785 99.270 51.927 2.919 132.849 -53.798 LYS 39 3.785 85.547 48.115 3.086 147.472 -52.556 LYS 40 3.785 86.846 56.607 3.105 138.553 -118.164 ILE 41 3.785 94.614 49.064 1.917 143.243 -104.324 GLU 42 3.785 83.812 56.085 2.440 160.828 -41.860 GLU 43 3.785 98.465 56.994 2.714 158.179 -74.861 LEU 44 3.785 86.063 38.858 2.074 176.659 102.329 GLY 45 3.786 97.537 133.746 0.000 0.000 180.000 GLY 46 3.784 117.437 63.081 0.000 0.000 180.000 GLY 47 3.785 91.425 68.516 0.000 0.000 180.000 GLY 48 3.785 136.496 20.218 0.000 0.000 180.000 GLU 49 3.784 90.762 -125.179 2.763 152.424 -134.490 VAL 50 3.785 89.897 122.644 1.460 142.703 -83.682 LYS 51 3.785 85.720 124.240 2.601 134.737 -146.671 LYS 52 3.785 81.391 86.531 3.094 143.151 -99.233 VAL 53 3.785 97.470 51.282 1.461 134.249 -62.621 GLU 54 3.786 93.331 48.720 2.564 146.346 -99.045 GLU 55 3.784 93.790 46.265 2.696 150.633 -59.911 GLU 56 3.785 83.606 49.391 2.055 169.300 -167.852 VAL 57 3.785 93.281 52.240 1.460 144.237 -96.089 LYS 58 3.785 86.192 47.933 2.934 153.109 -85.425 LYS 59 3.785 97.066 57.243 2.481 125.481 -24.034 LEU 60 3.785 81.584 62.431 2.157 146.082 -95.013 GLU 61 3.785 102.055 48.277 2.536 154.995 -88.741 GLU 62 3.785 88.204 47.695 2.324 141.973 -124.114 GLU 63 3.785 94.858 49.253 2.688 141.300 -43.881 ILE 64 3.785 94.414 33.242 1.910 142.265 -87.362 LYS 65 3.785 87.615 50.150 2.997 129.513 -40.349 LYS 66 3.785 85.747 53.802 3.065 150.194 -47.165 LEU 67 3.785 92.709 41.921 2.128 119.269 71.699 D 68 3.785 92.709 180.000 0.000 0.000 180.000 Potential energy and its components 4223.069527427199 1417.156941757942 245.1229503015478 -576.8404853557735 -443.4646226713600 0.0000000000000000 0.0000000000000000 -28.72282448527260 123.1100688267006 -29.22028710422527 0.0000000000000000 -77.01397934788042 107.3231863733070 90.31391374517578 8.996107713480077 0.0000000000000000 -45.58016651021919 1634.047527117884 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 Initial: Kinetic energy 110.2732342277786 potential energy 4223.069527427199 total energy 4333.342761654978 maximum acceleration 139.9965487157773 Momenta zeroed out, time 76.79 Momenta zeroed out, time 176.79 Momenta zeroed out, time 276.79 Momenta zeroed out, time 376.79 Momenta zeroed out, time 475.70 Momenta zeroed out, time 575.70 Momenta zeroed out, time 675.70 Momenta zeroed out, time 775.70 Momenta zeroed out, time 873.76 Momenta zeroed out, time 973.76 =================================== Timing =================================== MD calculations setup: 4.05000E+00 Energy & gradient evaluation: 1.40690E+02 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 MD steps: 1.42890E+02 ============================ End of MD calculation =========================== ***** Computation time: 0 hours 2 minutes 27 seconds *****