-------------------------------------------------------------------------------- FILE ASSIGNMENT -------------------------------------------------------------------------------- Input file : ala10-cx.inp Output file : ala10-cx.out_GB Sidechain potential file : ../../../../PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k 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 SCCOR parameter file : ../../../../PARAM/rotcorr_AM1.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 -------------------------------------------------------------------------------- ### LAST MODIFIED 03/28/12 23:29 by czarek ++++ Compile info ++++ Version 2.5 build 34 compiled Mon Apr 2 08:16:44 2012 compiled by adam@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: FC = ifort 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 ... CC = cc CFLAGS = -DLINUX -DPGI -c OPT = -O3 -ip -w LIBS = -Lxdrf -lxdrf 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_si... 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 ran_num 0.383569105241247 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: 10000 Initial time step of numerical integration: 0.10000 natural units 4.89000 fs Maximum acceleration threshold to reduce the time step/increase split number: 1.00000 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: 100 Frequency of coordinate output: 1000 Berendsen bath calculation Temperature: 300.00000 Coupling constant (tau): 0.10000 Momenta will be reset at zero every 1000 steps Velocities will be reset at random every 1000 steps ============================== End of MD run setup ============================= Energy-term weights (unscaled): WSCC= 1.352790 (SC-SC) WSCP= 1.593040 (SC-p) WELEC= 0.715340 (p-p electr) WVDWPP= 0.113710 (p-p VDW) WBOND= 1.000000 (stretching) WANG= 1.138730 (bending) WSCLOC= 0.162580 (SC local) WTOR= 1.985990 (torsional) WTORD= 1.570690 (double torsional) WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) WEL_LOC= 0.160360 (multi-body 3-rd order) WCORR4= 0.428870 (multi-body 4th order) WCORR5= 0.000000 (multi-body 5th order) WCORR6= 0.000000 (multi-body 6th order) WSCCOR= 1.000000 (back-scloc correlation) WTURN3= 1.687220 (turns, 3rd order) WTURN4= 0.662300 (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= 1.352790 (SC-SC) WSCP= 1.593040 (SC-p) WELEC= 0.715340 (p-p electr) WVDWPP= 0.113710 (p-p VDW) WBOND= 1.000000 (stretching) WANG= 1.138730 (bending) WSCLOC= 0.162580 (SC local) WTOR= 1.985990 (torsional) WTORD= 1.570690 (double torsional) WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) WEL_LOC= 0.160360 (multi-body 3-rd order) WCORR4= 0.428870 (multi-body 4th order) WCORR5= 0.000000 (multi-body 5th order) WCORR6= 0.000000 (multi-body 6th order) WSCCOR= 1.000000 (back-scloc correlatkion) WTURN3= 1.687220 (turns, 3rd order) WTURN4= 0.662300 (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 ITEL 1 21 0 2 9 1 3 9 1 4 9 1 5 9 1 6 9 1 7 9 1 8 9 1 9 9 1 10 9 1 11 9 0 ns= 0 iss: Boundaries in phi angle sampling: D 1 -180.0 180.0 ALA 2 -180.0 180.0 ALA 3 -180.0 180.0 ALA 4 -180.0 180.0 ALA 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 D 12 -180.0 180.0 NZ_START= 2 NZ_END= 11 IZ_SC= 0 Initial geometry will be read in. 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 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 ALA 5 3.800 90.000 180.000 0.743 100.000 -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 D 12 3.800 90.000 180.000 0.000 0.000 0.000 Mesoscopic molecular dynamics (MD) calculation. ******************************************************************************** Calling chainbuild ====================MD calculation start==================== Initial velocities randomly generated Initial velocities 0 -0.02571 0.04778 -0.01151 0.00000 0.00000 0.00000 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 2 -0.11082 -0.24316 -0.01092 -0.01544 0.04693 0.02901 3 0.17509 0.14021 0.01920 -0.06074 0.20983 -0.00546 4 -0.28110 -0.18298 0.04141 0.05768 -0.02663 -0.10403 5 0.52321 0.32791 -0.28506 0.24480 0.23049 0.08887 6 -0.24047 -0.12903 0.12193 0.03851 -0.08315 0.33390 7 0.09902 -0.00280 0.29189 -0.33532 -0.00436 0.03329 8 -0.12228 0.11945 -0.17716 0.08467 -0.09409 -0.31636 9 0.15147 -0.14801 -0.02818 0.01545 -0.19775 0.03783 10 0.03113 0.28957 -0.29450 0.09912 -0.08052 0.16164 11 0.00000 0.00000 0.00000 -0.24131 -0.01384 0.16566 12 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 Calling the zero-angular momentum subroutine vcm right after adjustment: -2.929524022998914E-017 -5.326407314543479E-018 -1.731082377226631E-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 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 ALA( 5) 7.60000 -7.60000 0.00000 7.25007 -7.43253 -0.63368 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 D ( 12) 22.80000 -19.00000 0.00000 22.80000 -19.00000 0.00000 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 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 ALA 5 3.800 90.000 180.000 0.743 100.000 -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 D 12 3.800 90.000 180.000 0.000 180.000 180.000 Potential energy and its components Virtual-chain energies: EVDW= -1.466547E+01 WEIGHT= 1.352790D+00 (SC-SC) EVDW2= 1.045502E+01 WEIGHT= 1.593040D+00 (SC-p) EES= -3.731028E+00 WEIGHT= 7.153400D-01 (p-p) EVDWPP= -1.171261E+01 WEIGHT= 1.137100D-01 (p-p VDW) ESTR= 1.531499E-27 WEIGHT= 1.000000D+00 (stretching) EBE= -2.106038E+00 WEIGHT= 1.138730D+00 (bending) ESC= 9.424775E+01 WEIGHT= 1.625800D-01 (SC local) ETORS= 0.000000E+00 WEIGHT= 1.985990D+00 (torsional) ETORSD= -9.403905E-01 WEIGHT= 1.570690D+00 (double torsional) EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) ECORR4= -2.225631E+00 WEIGHT= 4.288700D-01 (multi-body) ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) EELLO= 1.644793E+01 WEIGHT= 1.603600D-01 (electrostatic-local) ETURN3= -1.490245E+00 WEIGHT= 1.687220D+00 (turns, 3rd order) ETURN4= 6.106256E+00 WEIGHT= 6.623000D-01 (turns, 4th order) ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order) ESCCOR= 0.000000E+00 WEIGHT= 1.000000D+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= 7.475595E+00 (total) Initial: Kinetic energy 1.64667E+01 potential energy 7.47559E+00 total energy 2.39423E+01 maximum acceleration 9.73465E-01 Velocities reset to random values, time 84.93 Momenta zeroed out, time 84.93 Velocities reset to random values, time 162.90 Momenta zeroed out, time 162.90 Velocities reset to random values, time 249.85 Momenta zeroed out, time 249.85 Velocities reset to random values, time 319.31 Momenta zeroed out, time 319.31 Velocities reset to random values, time 398.92 Momenta zeroed out, time 398.92 Velocities reset to random values, time 476.10 Momenta zeroed out, time 476.10 Velocities reset to random values, time 540.82 Momenta zeroed out, time 540.82 Velocities reset to random values, time 612.01 Momenta zeroed out, time 612.01 Velocities reset to random values, time 687.88 Momenta zeroed out, time 687.88 Velocities reset to random values, time 762.77 Momenta zeroed out, time 762.77 =================================== Timing =================================== MD calculations setup: 0.00000E+00 Energy & gradient evaluation: 7.80000E-01 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 MD steps: 8.80000E-01 ============================ End of MD calculation =========================== ***** Computation time: 0 hours 0 minutes 1 seconds *****