X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=examples%2Funres%2FMD%2Fff_gab%2Fala10-cx.out_GB;fp=examples%2Funres%2FMD%2Fff_gab%2Fala10-cx.out_GB;h=0000000000000000000000000000000000000000;hp=68334349f8ef3303ab7af4bf66439dfa9533b12a;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/examples/unres/MD/ff_gab/ala10-cx.out_GB b/examples/unres/MD/ff_gab/ala10-cx.out_GB deleted file mode 100644 index 6833434..0000000 --- a/examples/unres/MD/ff_gab/ala10-cx.out_GB +++ /dev/null @@ -1,309 +0,0 @@ --------------------------------------------------------------------------------- - 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 *****