X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=examples%2Funres%2FMD%2FLangevin%2Fff_1l2y%2Foutputs%2F1L2Y_MD.out_GB000;fp=examples%2Funres%2FMD%2FLangevin%2Fff_1l2y%2Foutputs%2F1L2Y_MD.out_GB000;h=45a1078a6c598f5b991c39650635e681c001a034;hp=0000000000000000000000000000000000000000;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/examples/unres/MD/Langevin/ff_1l2y/outputs/1L2Y_MD.out_GB000 b/examples/unres/MD/Langevin/ff_1l2y/outputs/1L2Y_MD.out_GB000 new file mode 100644 index 0000000..45a1078 --- /dev/null +++ b/examples/unres/MD/Langevin/ff_1l2y/outputs/1L2Y_MD.out_GB000 @@ -0,0 +1,441 @@ +-------------------------------------------------------------------------------- + FILE ASSIGNMENT +-------------------------------------------------------------------------------- + Input file : 1L2Y_MD.inp + Output file : 1L2Y_MD.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 + +Langevin dynamics calculation with direct integration of Langevin equations + + Temperature: 300.00000 + Viscosity of the solvent: 0.89040 + Radius of solvent molecule: 1.40000 + Scaling factor of the friction forces: 0.02000 + Eta of the solvent in natural units: 49.27846 + +Radii of site types and friction coefficients and std's of stochastic forces of fully exposed sites + + p 2.50 3.84372 4.78549 + CYS 5.00 6.30764 6.13033 + MET 6.20 7.49033 6.68037 + PHE 6.80 8.08167 6.93906 + ILE 6.20 7.49033 6.68037 + LEU 6.30 7.58888 6.72418 + VAL 5.80 7.09610 6.50220 + TRP 7.20 8.47589 7.10629 + TYR 6.90 8.18022 6.98124 + ALA 4.60 5.91342 5.93567 + GLY 3.80 5.12496 5.52580 + THR 5.60 6.89898 6.41125 + SER 4.80 6.11053 6.03378 + GLN 6.10 7.39177 6.63628 + ASN 5.70 6.99754 6.45688 + GLU 6.10 7.39177 6.63628 + ASP 5.60 6.89898 6.41125 + HIS 6.20 7.49033 6.68037 + ARG 6.80 8.08167 6.93906 + LYS 6.30 7.58888 6.72418 + PRO 5.60 6.89898 6.41125 + +============================== End of MD 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 +Extended chain initial geometry. + +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 3.800 0.000 0.000 1.684 110.000 -120.000 +LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000 +TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000 +ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000 +GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000 +TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000 +LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000 +LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000 +ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000 +GLY 11 3.800 90.000 180.000 0.000 110.000 -120.000 +GLY 12 3.800 90.000 180.000 0.000 110.000 -120.000 +PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000 +SER 14 3.800 90.000 180.000 1.150 110.000 -120.000 +SER 15 3.800 90.000 180.000 1.150 110.000 -120.000 +GLY 16 3.800 90.000 180.000 0.000 110.000 -120.000 +ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000 +PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000 +PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000 +PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000 +SER 21 3.800 90.000 180.000 1.150 110.000 -120.000 +D 22 3.800 90.000 180.000 0.000 0.000 0.000 + + +******************************************************************************** + Processor 0: end reading molecular data. +******************************************************************************** + + +Mesoscopic molecular dynamics (MD) calculation. + +******************************************************************************** + + Calling chainbuild +====================MD calculation start==================== + Initial velocities randomly generated + Initial velocities + 0 0.02267 0.06282 -0.18129 0.00000 0.00000 0.00000 + 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 2 -0.36014 -0.22705 -0.00171 -0.06904 -0.02446 0.24778 + 3 0.27655 0.20645 0.14150 0.26200 0.15105 0.09342 + 4 0.10834 -0.11941 0.14712 0.10330 -0.09595 0.03277 + 5 0.05798 -0.08974 0.08325 0.03879 0.02648 -0.14707 + 6 0.01211 0.16444 -0.14711 -0.01628 0.11599 -0.16511 + 7 -0.01010 -0.05513 0.03662 -0.18958 0.06429 0.04531 + 8 -0.01799 0.13439 -0.04510 0.02318 0.10657 0.03722 + 9 -0.26458 -0.01929 0.09531 -0.22533 -0.17075 -0.04594 + 10 0.14062 -0.06051 -0.18363 0.20415 -0.15549 -0.17329 + 11 -0.14145 0.13159 -0.00733 0.00000 0.00000 0.00000 + 12 0.19745 -0.24261 0.01759 0.00000 0.00000 0.00000 + 13 -0.15305 0.28008 0.07251 0.06558 0.14824 0.10057 + 14 0.11104 -0.31941 0.15684 -0.02949 -0.09688 0.05398 + 15 0.14534 0.10342 -0.23754 -0.13923 0.07952 0.07655 + 16 -0.11969 0.14757 0.15002 0.00000 0.00000 0.00000 + 17 -0.09007 -0.15856 -0.20234 -0.07955 -0.08516 -0.10245 + 18 0.24139 0.09063 0.14043 -0.02074 0.10220 0.04907 + 19 -0.14354 -0.07226 -0.29143 -0.12408 -0.06855 -0.02978 + 20 0.28536 0.09023 0.56577 0.02348 0.16297 0.19270 + 21 0.00000 0.00000 0.00000 -0.13725 -0.06434 -0.21957 + 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + Calling the zero-angular momentum subroutine + vcm right after adjustment: + 1.837610523517500E-017 -2.960594732333751E-018 9.596410511702503E-018 + + + 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) 3.80000 0.00000 0.00000 3.64779 0.96674 1.37044 +LEU( 3) 3.80000 -3.80000 0.00000 2.68687 -3.62474 -1.57795 +TYR( 4) 7.60000 -3.80000 0.00000 7.37548 -2.37399 2.02147 +ILE( 5) 7.60000 -7.60000 0.00000 6.58044 -7.43947 -1.44530 +GLN( 6) 11.40000 -7.60000 0.00000 11.19753 -6.31407 1.82291 +TRP( 7) 11.40000 -11.40000 0.00000 9.90453 -11.16454 -2.11994 +LEU( 8) 15.20000 -11.40000 0.00000 15.02474 -10.28687 1.57795 +LYS( 9) 15.20000 -15.20000 0.00000 13.74127 -14.97033 -2.06786 +ASP( 10) 19.00000 -15.20000 0.00000 18.84553 -14.21890 1.39078 +GLY( 11) 19.00000 -19.00000 0.00000 19.00000 -19.00000 0.00000 +GLY( 12) 22.80000 -19.00000 0.00000 22.80000 -19.00000 0.00000 +PRO( 13) 22.80000 -22.80000 0.00000 22.02787 -22.67843 -1.09456 +SER( 14) 26.60000 -22.80000 0.00000 26.49606 -22.13981 0.93587 +SER( 15) 26.60000 -26.60000 0.00000 25.93981 -26.49606 -0.93587 +GLY( 16) 30.40000 -26.60000 0.00000 30.40000 -26.60000 0.00000 +ARG( 17) 30.40000 -30.40000 0.00000 28.66629 -30.12703 -2.45767 +PRO( 18) 34.20000 -30.40000 0.00000 34.07843 -29.62787 1.09456 +PRO( 19) 34.20000 -34.20000 0.00000 33.42787 -34.07843 -1.09456 +PRO( 20) 38.00000 -34.20000 0.00000 37.87843 -33.42787 1.09456 +SER( 21) 38.00000 -38.00000 0.00000 37.33981 -37.89606 -0.93587 +D ( 22) 41.80000 -38.00000 0.00000 41.80000 -38.00000 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 +ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000 +LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000 +TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000 +ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000 +GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000 +TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000 +LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000 +LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000 +ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000 +GLY 11 3.800 90.000 180.000 0.000 180.000 180.000 +GLY 12 3.800 90.000 180.000 0.000 180.000 180.000 +PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000 +SER 14 3.800 90.000 180.000 1.150 110.000 -120.000 +SER 15 3.800 90.000 180.000 1.150 110.000 -120.000 +GLY 16 3.800 90.000 180.000 0.000 180.000 180.000 +ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000 +PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000 +PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000 +PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000 +SER 21 3.800 90.000 180.000 1.150 110.000 -120.000 +D 22 3.800 90.000 180.000 0.000 180.000 180.000 + Potential energy and its components + +Virtual-chain energies: + +EVDW= -1.947821E+01 WEIGHT= 1.000000D+00 (SC-SC) +EVDW2= 2.387106E+01 WEIGHT= 1.233150D+00 (SC-p) +EES= -7.520330E+00 WEIGHT= 8.447600D-01 (p-p) +EVDWPP= -2.624923E+01 WEIGHT= 2.317300D-01 (p-p VDW) +ESTR= 1.118676E+02 WEIGHT= 1.000000D+00 (stretching) +EBE= -1.933948E+01 WEIGHT= 6.295400D-01 (bending) +ESC= 8.868295E+01 WEIGHT= 1.055400D-01 (SC local) +ETORS= 2.664535E-15 WEIGHT= 1.843160D+00 (torsional) +ETORSD= -2.547586E+00 WEIGHT= 1.265710D+00 (double torsional) +EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) +ECORR4= -4.501075E+00 WEIGHT= 1.921200D-01 (multi-body) +ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +EELLO= 2.197932E+01 WEIGHT= 3.735700D-01 (electrostatic-local) +ETURN3= -1.258124E+00 WEIGHT= 1.403230D+00 (turns, 3rd order) +ETURN4= 9.498513E+00 WEIGHT= 6.467300D-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= 1.150741E+02 (total) + +Initial: + Kinetic energy 3.16218E+01 + potential energy 1.15074E+02 + total energy 1.46696E+02 + + maximum acceleration 4.85027E+00 + + + +=================================== Timing =================================== + + MD calculations setup: 7.81250E-03 + Energy & gradient evaluation: 3.78934E+02 + Stochastic MD setup: 0.00000E+00 + Stochastic MD step setup: 0.00000E+00 + MD steps: 4.56156E+02 + + +============================ End of MD calculation =========================== +CG processor 0 is finishing work. + Total wall clock time 456.886718750000 sec