--- /dev/null
+--------------------------------------------------------------------------------
+ FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file : small.inp
+ Output file : small.out_GB000
+
+ Sidechain potential file :
+ /users/czarek/UNRES/GIT/unres/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-
+ 10-8k
+ SCp potential file : /users/czarek/UNRES/GIT/unres/PARAM/scp.parm
+ Electrostatic potential file :
+ /users/czarek/UNRES/GIT/unres/PARAM/electr_631Gdp.parm
+ Cumulant coefficient file :
+ /users/czarek/UNRES/GIT/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3
+ Torsional parameter file :
+ /users/czarek/UNRES/GIT/unres/PARAM/torsion_631Gdp.parm
+ Double torsional parameter file :
+ /users/czarek/UNRES/GIT/unres/PARAM/torsion_double_631Gdp.parm
+ SCCOR parameter file : /users/czarek/UNRES/GIT/unres/PARAM/sccor_pdb_shelly.dat
+ Bond & inertia constant file : /users/czarek/UNRES/GIT/unres/PARAM/bond.parm
+ Bending parameter file :
+ /users/czarek/UNRES/GIT/unres/PARAM/thetaml.5parm
+ Rotamer parameter file :
+ /users/czarek/UNRES/GIT/unres/PARAM/scgauss.parm
+ Threading database :
+ /users/czarek/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 3.1 build 52
+ compiled Sun Feb 17 00:55:22 2013
+ compiled by czarek@piasek3
+ OS name: Linux
+ OS release: 2.6.32-42-generic
+ OS version: #96-Ubuntu SMP Wed Aug 15 19:37:37 UTC 2012
+ flags:
+ INSTALL_DIR = /users/software/mpich-1.2.7p1_int...
+ FC= ifort
+ OPT = -O3 -ip
+ FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+ FFLAGS1 = -c -g -CA -CB -I$(INSTALL_DIR)/inclu...
+ FFLAGS2 = -c -g -O0 -I$(INSTALL_DIR)/include
+ FFLAGSE = -c -O3 -ipo -opt_report -I$(INSTALL...
+ LIBS = -L$(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 ++++
+
+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 -16
+ -62756
+ 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: 100000
+ Initial time step of numerical integration: 0.01000 natural units
+ 0.48900 fs
+Maximum acceleration threshold to reduce the time step/increase split number: 5.00000
+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: 500
+Microcanonical mode calculation
+
+============================== 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= 0.000000 (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= 0.000000 (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 11.1621168104436 AKTH
+ 8.13134337184633 AKCT 8.87055640565054
+ V1SS -0.798350076508549 V2SS 5.62541118725005 V3SS
+ 10.1272185631177
+ EBR -5.50000000000000 SS_DEPTH -5.46701011744817
+ HT -1.40133843152500
+PDB data will be read from file a.pdb
+ Nres: 18
+Backbone and SC coordinates as read from the PDB
+ 1 10 GLY -11.849 6.596 -2.403 -11.849 6.596 -2.403
+ 2 9 ALA -13.418 6.572 -5.919 -12.908 6.747 -6.410
+ 3 9 ALA -16.143 3.889 -6.138 -16.793 4.183 -6.397
+ 4 9 ALA -13.520 1.166 -6.550 -12.785 1.239 -6.559
+ 5 1 CYS -12.629 1.631 -2.805 -13.518 2.576 -2.698
+ 6 9 ALA -13.467 -2.136 -2.650 -13.490 -2.860 -2.729
+ 7 9 ALA -11.256 -2.842 -5.622 -11.072 -2.578 -6.320
+ 8 9 ALA -8.206 -2.125 -3.496 -8.226 -1.485 -3.216
+ 9 9 ALA -9.298 -4.587 -0.877 -9.634 -4.348 -0.224
+ 10 9 ALA -10.565 -6.979 -3.578 -10.220 -7.012 -4.281
+ 11 9 ALA -9.060 -10.399 -3.347 -9.290 -11.104 -3.486
+ 12 9 ALA -5.538 -8.995 -3.201 -5.545 -8.635 -3.863
+ 13 9 ALA -4.176 -7.434 -0.023 -3.823 -8.014 0.272
+ 14 1 CYS -3.957 -3.989 1.621 -5.048 -3.526 1.725
+ 15 9 ALA -3.473 -3.009 5.302 -3.003 -3.112 5.889
+ 16 9 ALA -3.888 0.809 5.844 -4.524 1.149 5.521
+ 17 9 ALA -3.394 0.685 9.610 -2.879 0.254 9.328
+ 18 10 GLY -3.341 3.372 12.241 -3.341 3.372 12.241
+nsup= 18 nstart_sup= 1
+ After sideadd
+
+Geometry of the virtual chain.
+ Res d Theta Gamma Dsc Alpha Beta
+GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
+ALA 2 3.850 0.000 0.000 0.729 146.694 -109.363
+ALA 3 3.830 110.272 0.000 0.759 147.957 -128.746
+ALA 4 3.803 90.977 -78.713 0.739 105.672 -50.865
+CYS 5 3.878 88.166 72.402 1.302 112.139 -116.564
+ALA 6 3.862 82.642 123.024 0.729 120.951 3.720
+ALA 7 3.771 91.361 49.351 0.769 137.392 -55.570
+ALA 8 3.786 89.674 70.311 0.699 119.648 -87.119
+ALA 9 3.757 91.902 53.321 0.772 145.673 -99.574
+ALA 10 3.824 90.793 38.471 0.784 108.765 -64.768
+ALA 11 3.744 113.246 124.426 0.754 167.686 -74.150
+ALA 12 3.794 92.149 -50.745 0.754 133.580 -108.877
+ALA 13 3.794 121.181 76.519 0.740 168.142 -147.575
+CYS 14 3.823 138.722 -91.423 1.190 108.677 -76.446
+ALA 15 3.840 130.494 158.051 0.759 141.443 -47.832
+ALA 16 3.879 111.821 -172.250 0.790 136.439 -94.007
+ALA 17 3.800 95.305 177.774 0.728 120.497 -127.361
+GLY 18 3.761 132.203 178.798 0.000 0.000 0.000
+ ITEL
+ 1 10 1
+ 2 9 1
+ 3 9 1
+ 4 9 1
+ 5 1 1
+ 6 9 1
+ 7 9 1
+ 8 9 1
+ 9 9 1
+ 10 9 1
+ 11 9 1
+ 12 9 1
+ 13 9 1
+ 14 1 1
+ 15 9 1
+ 16 9 1
+ 17 9 1
+ ns= 2 iss: 5 14
+ nss= 0 ihpb,jhpb:
+Boundaries in phi angle sampling:
+GLY 1 -180.0 180.0
+ALA 2 -180.0 180.0
+ALA 3 -180.0 180.0
+ALA 4 -180.0 180.0
+CYS 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
+ALA 12 -180.0 180.0
+ALA 13 -180.0 180.0
+CYS 14 -180.0 180.0
+ALA 15 -180.0 180.0
+ALA 16 -180.0 180.0
+ALA 17 -180.0 180.0
+GLY 18 -180.0 180.0
+ NZ_START= 1 NZ_END= 18
+ IZ_SC= 0
+
+Geometry of the virtual chain.
+ Res d Theta Gamma Dsc Alpha Beta
+GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
+ALA 2 3.850 0.000 0.000 0.729 146.694 -109.363
+ALA 3 3.830 110.272 0.000 0.759 147.957 -128.746
+ALA 4 3.803 90.977 -78.713 0.739 105.672 -50.865
+CYS 5 3.878 88.166 72.402 1.302 112.139 -116.564
+ALA 6 3.862 82.642 123.024 0.729 120.951 3.720
+ALA 7 3.771 91.361 49.351 0.769 137.392 -55.570
+ALA 8 3.786 89.674 70.311 0.699 119.648 -87.119
+ALA 9 3.757 91.902 53.321 0.772 145.673 -99.574
+ALA 10 3.824 90.793 38.471 0.784 108.765 -64.768
+ALA 11 3.744 113.246 124.426 0.754 167.686 -74.150
+ALA 12 3.794 92.149 -50.745 0.754 133.580 -108.877
+ALA 13 3.794 121.181 76.519 0.740 168.142 -147.575
+CYS 14 3.823 138.722 -91.423 1.190 108.677 -76.446
+ALA 15 3.840 130.494 158.051 0.759 141.443 -47.832
+ALA 16 3.879 111.821 -172.250 0.790 136.439 -94.007
+ALA 17 3.800 95.305 177.774 0.728 120.497 -127.361
+GLY 18 3.761 132.203 178.798 0.000 0.000 0.000
+
+The chain contains 2 disulfide-bridging cysteines.
+ 5 14
+ Running with dynamic disulfide-bond formation
+ Processor 0 CG group 0 absolute rank 0 nhpb
+ 0 link_start= 1 link_end 0
+
+
+********************************************************************************
+ Processor 0: end reading molecular data.
+********************************************************************************
+
+
+Mesoscopic molecular dynamics (MD) calculation.
+
+********************************************************************************
+
+ Calling chainbuild
+====================MD calculation start====================
+ Initial velocities randomly generated
+ Initial velocities
+ 0 0.33890 0.02320 0.23659 0.00000 0.00000 0.00000
+ 1 -0.15077 -0.23023 -0.18811 0.00000 0.00000 0.00000
+ 2 -0.14850 0.36395 0.17819 -0.06593 0.14268 0.01033
+ 3 -0.01216 -0.31272 -0.40265 -0.27199 0.03880 -0.26248
+ 4 0.13139 0.25689 0.25345 -0.06906 0.09806 0.19560
+ 5 -0.27858 -0.01261 0.04461 -0.15425 -0.01325 -0.02214
+ 6 0.09914 0.11979 0.14915 -0.11171 -0.17646 -0.10207
+ 7 -0.15740 -0.32760 -0.08342 -0.15559 -0.17162 -0.27142
+ 8 -0.01757 0.19689 -0.31981 -0.04208 0.07236 -0.23178
+ 9 0.29843 -0.21826 0.12725 0.01235 -0.10442 -0.18484
+ 10 -0.35680 0.17980 -0.11210 -0.00509 -0.02006 0.01600
+ 11 0.42311 -0.07463 0.22371 0.30508 -0.03813 0.04260
+ 12 -0.28440 -0.17000 -0.23671 -0.06923 -0.11283 -0.12729
+ 13 0.12013 0.21611 0.14782 0.07641 0.09993 0.18719
+ 14 0.15808 0.02556 -0.12952 -0.10167 -0.08786 -0.15044
+ 15 -0.16543 -0.08643 0.20762 0.03124 -0.00978 0.12744
+ 16 0.07008 0.14536 -0.28387 0.01006 0.26396 -0.15863
+ 17 -0.12394 -0.22493 0.30015 -0.38318 -0.15223 0.30217
+ 18 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
+ Calling the zero-angular momentum subroutine
+ vcm right after adjustment:
+ 5.424257488318338E-018 -6.299137728369682E-018 1.504794012888313E-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
+ALA( 2) 3.85027 0.00000 0.00000 4.08973 0.57597 0.37779
+ALA( 3) 5.17743 -3.59315 0.00000 5.67699 -3.69784 -0.56169
+ALA( 4) 4.50175 -3.91184 3.72914 4.21000 -3.40822 4.18399
+CYS( 5) 0.71590 -4.05898 2.90403 0.97457 -3.92549 1.63515
+ALA( 6) 0.93933 -7.41535 4.80177 1.02535 -7.94644 5.29318
+ALA( 7) 2.75671 -5.77560 7.67023 3.31749 -5.27434 7.82844
+ALA( 8) -0.43207 -3.97536 8.63318 -0.68360 -3.58848 8.10834
+ALA( 9) -2.36335 -7.19560 8.74835 -2.82423 -7.40238 8.16418
+ALA( 10) 0.63437 -8.99997 10.29116 1.13596 -8.62055 10.75890
+ALA( 11) -0.16855 -10.69479 13.53118 0.05650 -11.32099 13.88681
+ALA( 12) -1.74585 -7.54908 14.95019 -1.14072 -7.10241 14.90335
+ALA( 13) -5.21270 -6.43737 13.88410 -5.62232 -6.73606 14.42357
+CYS( 14) -6.82468 -4.19410 11.24062 -6.47796 -4.54138 10.15681
+ALA( 15) -10.38945 -4.18760 9.81345 -11.11637 -4.14078 10.02669
+ALA( 16) -10.73908 -1.74754 6.81896 -10.18707 -1.79179 6.25526
+ALA( 17) -14.37866 -2.58026 6.11029 -14.32832 -2.51011 6.83351
+GLY( 18) -16.81959 -1.27490 3.56414 -16.81959 -1.27490 3.56414
+
+Geometry of the virtual chain.
+ Res d Theta Gamma Dsc Alpha Beta
+GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
+ALA 2 3.850 0.000 0.000 0.729 146.694 -109.363
+ALA 3 3.830 110.272 0.000 0.759 147.957 -128.746
+ALA 4 3.803 90.977 -78.713 0.739 105.672 -50.865
+CYS 5 3.878 88.166 72.402 1.302 112.139 -116.564
+ALA 6 3.862 82.642 123.024 0.729 120.951 3.720
+ALA 7 3.771 91.361 49.351 0.769 137.392 -55.570
+ALA 8 3.786 89.674 70.311 0.699 119.648 -87.119
+ALA 9 3.757 91.902 53.321 0.772 145.673 -99.574
+ALA 10 3.824 90.793 38.471 0.784 108.765 -64.768
+ALA 11 3.744 113.246 124.426 0.754 167.686 -74.150
+ALA 12 3.794 92.149 -50.745 0.754 133.580 -108.877
+ALA 13 3.794 121.181 76.519 0.740 168.142 -147.575
+CYS 14 3.823 138.722 -91.423 1.190 108.677 -76.446
+ALA 15 3.840 130.494 158.051 0.759 141.443 -47.832
+ALA 16 3.879 111.821 -172.250 0.790 136.439 -94.007
+ALA 17 3.800 95.305 177.774 0.728 120.497 -127.361
+GLY 18 3.761 132.203 178.798 0.000 180.000 180.000
+ Potential energy and its components
+
+Virtual-chain energies:
+
+EVDW= -3.681888E+01 WEIGHT= 1.352790E+00 (SC-SC)
+EVDW2= 2.935543E+01 WEIGHT= 1.593040E+00 (SC-p)
+EES= -5.873651E+01 WEIGHT= 7.153400E-01 (p-p)
+EVDWPP= -2.078573E+01 WEIGHT= 1.137100E-01 (p-p VDW)
+ESTR= 1.126963E+01 WEIGHT= 1.000000E+00 (stretching)
+EBE= -2.163931E+01 WEIGHT= 1.138730E+00 (bending)
+ESC= 8.185684E+01 WEIGHT= 1.625800E-01 (SC local)
+ETORS= 1.409747E+01 WEIGHT= 1.985990E+00 (torsional)
+ETORSD= 3.856076E-01 WEIGHT= 1.570690E+00 (double torsional)
+EHPB= 0.000000E+00 WEIGHT= 1.000000E+00 (SS bridges & dist. cnstr.)
+ECORR4= -3.806576E+01 WEIGHT= 4.288700E-01 (multi-body)
+ECORR5= 0.000000E+00 WEIGHT= 0.000000E+00 (multi-body)
+ECORR6= 0.000000E+00 WEIGHT= 0.000000E+00 (multi-body)
+EELLO= 5.874355E+00 WEIGHT= 1.603600E-01 (electrostatic-local)
+ETURN3= 1.472773E+01 WEIGHT= 1.687220E+00 (turns, 3rd order)
+ETURN4= -3.305062E+00 WEIGHT= 6.623000E-01 (turns, 4th order)
+ETURN6= 0.000000E+00 WEIGHT= 0.000000E+00 (turns, 6th order)
+ESCCOR= 0.000000E+00 WEIGHT= 0.000000E+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= -1.160756E+01 (total)
+
+Initial:
+ Kinetic energy 2.82436E+01
+ potential energy -1.16076E+01
+ total energy 1.66360E+01
+
+ maximum acceleration 1.95619E+00
+
+ SSBOND_FORM 129.12 300.0 5 14
+ SSBOND_BREAK 134.81 300.0 5 14
+ SSBOND_FORM 178.26 300.0 5 14
+ SSBOND_BREAK 180.34 300.0 5 14
+ SSBOND_FORM 253.52 300.0 5 14
+ SSBOND_BREAK 258.40 300.0 5 14
+ SSBOND_FORM 420.52 300.0 5 14
+ SSBOND_BREAK 421.60 300.0 5 14
+ SSBOND_FORM 425.82 300.0 5 14
+ SSBOND_BREAK 428.19 300.0 5 14
+ SSBOND_FORM 494.06 300.0 5 14
+ SSBOND_BREAK 496.25 300.0 5 14
+ SSBOND_FORM 500.25 300.0 5 14
+ SSBOND_BREAK 500.33 300.0 5 14
+ SSBOND_FORM 500.82 300.0 5 14
+ SSBOND_BREAK 501.09 300.0 5 14
+ SSBOND_FORM 520.74 300.0 5 14
+ SSBOND_BREAK 570.42 300.0 5 14
+ SSBOND_FORM 628.51 300.0 5 14
+ SSBOND_BREAK 630.04 300.0 5 14
+ SSBOND_FORM 634.06 300.0 5 14
+ SSBOND_BREAK 638.66 300.0 5 14
+ SSBOND_FORM 660.47 300.0 5 14
+ SSBOND_BREAK 661.56 300.0 5 14
+ SSBOND_FORM 671.40 300.0 5 14
+ SSBOND_BREAK 673.68 300.0 5 14
+ SSBOND_FORM 697.08 300.0 5 14
+ SSBOND_BREAK 699.21 300.0 5 14
+ SSBOND_FORM 699.76 300.0 5 14
+ SSBOND_BREAK 700.73 300.0 5 14
+ SSBOND_FORM 711.03 300.0 5 14
+ SSBOND_BREAK 713.24 300.0 5 14
+ SSBOND_FORM 714.76 300.0 5 14
+ SSBOND_BREAK 717.99 300.0 5 14
+ SSBOND_FORM 724.88 300.0 5 14
+ SSBOND_BREAK 749.39 300.0 5 14
+ SSBOND_FORM 789.73 300.0 5 14
+ SSBOND_BREAK 793.20 300.0 5 14
+
+
+=================================== Timing ===================================
+
+ MD calculations setup: 7.81250E-03
+ Energy & gradient evaluation: 1.83398E+01
+ Stochastic MD setup: 0.00000E+00
+ Stochastic MD step setup: 0.00000E+00
+ MD steps: 2.24727E+01
+
+
+============================ End of MD calculation ===========================
+CG processor 0 is finishing work.
+ Total wall clock time 22.5898437500000 sec
projects / unres.git / blobdiff