--- /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 41
+ compiled Fri Feb 15 01:43:03 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 -w
+ 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 ++++
+
+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: 500
+ Initial time step of numerical integration: 0.10000 natural units
+ 4.89000 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: 1
+ Frequency of coordinate output: 300
+Berendsen bath calculation
+ Temperature: 300.00000
+ Coupling constant (tau): 1.00000
+Momenta will be reset at zero every 1000 steps
+
+===== Calculation restarted ====
+
+
+============================== 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 15.1000000000000 AKTH
+ 11.0000000000000 AKCT 12.0000000000000
+ V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
+ 13.7000000000000
+ EBR -5.50000000000000 SS_DEPTH -7.39571661678271
+ HT 0.000000000000000E+000
+PDB data will be read from file ss.pdb
+ Nres: 18
+Backbone and SC coordinates as read from the PDB
+ 1 10 GLY 18.887 -10.163 -10.608 18.887 -10.163 -10.608
+ 2 9 ALA 18.562 -9.885 -6.834 18.353 -9.134 -6.608
+ 3 9 ALA 16.754 -11.361 -3.915 16.860 -12.098 -3.836
+ 4 9 ALA 16.762 -9.897 -0.433 16.145 -9.572 -0.328
+ 5 1 CYS 15.755 -12.524 2.082 16.051 -13.633 1.487
+ 6 9 ALA 15.104 -12.916 5.816 14.965 -12.382 6.257
+ 7 9 ALA 12.233 -15.298 5.159 11.752 -15.096 4.590
+ 8 9 ALA 12.615 -18.906 4.131 12.996 -18.890 4.861
+ 9 9 ALA 9.909 -21.356 3.181 9.333 -20.985 3.212
+ 10 9 ALA 10.743 -20.954 -0.478 10.850 -20.324 -0.915
+ 11 9 ALA 12.566 -23.869 -1.971 12.731 -24.062 -2.616
+ 12 9 ALA 15.810 -21.927 -1.726 15.774 -21.687 -2.426
+ 13 9 ALA 18.582 -20.075 0.198 19.150 -20.569 0.255
+ 14 1 CYS 19.577 -16.394 -0.296 18.494 -15.682 -0.508
+ 15 9 ALA 22.406 -14.224 1.116 23.137 -14.120 1.199
+ 16 9 ALA 22.651 -10.366 0.632 22.481 -9.688 0.945
+ 17 9 ALA 25.991 -8.590 0.178 26.589 -8.669 0.306
+ 18 10 GLY 26.757 -7.435 -3.316 26.757 -7.435 -3.316
+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 3.798 0.000 0.000 0.812 126.829 -76.902
+ALA 3 3.737 142.050 0.000 0.749 137.463 -84.306
+ALA 4 3.777 124.464 -169.125 0.705 105.294 -78.108
+CYS 5 3.774 110.120 -160.528 1.293 158.619 -104.565
+ALA 6 3.811 140.379 -177.281 0.706 135.838 -82.329
+ALA 7 3.788 91.388 142.499 0.772 126.337 -76.931
+ALA 8 3.771 124.902 75.891 0.824 113.900 -118.360
+ALA 9 3.772 128.130 -174.931 0.686 107.064 -87.141
+ALA 10 3.774 90.943 102.826 0.774 157.826 -59.303
+ALA 11 3.748 114.254 105.902 0.693 119.632 -54.909
+ALA 12 3.789 89.544 -101.667 0.741 155.157 -110.619
+ALA 13 3.849 153.580 60.970 0.755 140.632 -99.009
+CYS 14 3.845 125.646 -120.233 1.313 150.049 -92.166
+ALA 15 3.835 133.262 -173.688 0.743 134.737 -34.633
+ALA 16 3.896 124.125 -171.229 0.766 131.592 -41.437
+ALA 17 3.810 122.109 -144.160 0.617 138.711 -49.120
+GLY 18 3.759 115.636 105.386 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= 1 ihpb,jhpb: 5 14
+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
+ Processor 0 CG group 0 absolute rank 0 nhpb
+ 1 link_start= 1 link_end 1
+
+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 3.798 0.000 0.000 0.812 126.829 -76.902
+ALA 3 3.737 142.050 0.000 0.749 137.463 -84.306
+ALA 4 3.777 124.464 -169.125 0.705 105.294 -78.108
+CYS 5 3.774 110.120 -160.528 1.293 158.619 -104.565
+ALA 6 3.811 140.379 -177.281 0.706 135.838 -82.329
+ALA 7 3.788 91.388 142.499 0.772 126.337 -76.931
+ALA 8 3.771 124.902 75.891 0.824 113.900 -118.360
+ALA 9 3.772 128.130 -174.931 0.686 107.064 -87.141
+ALA 10 3.774 90.943 102.826 0.774 157.826 -59.303
+ALA 11 3.748 114.254 105.902 0.693 119.632 -54.909
+ALA 12 3.789 89.544 -101.667 0.741 155.157 -110.619
+ALA 13 3.849 153.580 60.970 0.755 140.632 -99.009
+CYS 14 3.845 125.646 -120.233 1.313 150.049 -92.166
+ALA 15 3.835 133.262 -173.688 0.743 134.737 -34.633
+ALA 16 3.896 124.125 -171.229 0.766 131.592 -41.437
+ALA 17 3.810 122.109 -144.160 0.617 138.711 -49.120
+GLY 18 3.759 115.636 105.386 0.000 0.000 0.000
+
+The chain contains 2 disulfide-bridging cysteines.
+ 5 14
+
+Pre-formed links are:
+
+CYS( 5) -- CYS( 14) 0.000 -5.500 0.000
+
+
+
+********************************************************************************
+ Processor 0: end reading molecular data.
+********************************************************************************
+
+
+Mesoscopic molecular dynamics (MD) calculation.
+
+********************************************************************************
+
+ Calling chainbuild
+====================MD calculation start====================
+ File small_000.rst does not exist
+ 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:
+ -1.942234132913985E-017 -2.274688624133496E-018 -1.784755689704743E-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) 3.79816 0.00000 0.00000 4.09557 0.41221 0.63276
+ALA( 3) 6.74526 -2.29838 0.00000 6.76075 -2.76877 -0.58236
+ALA( 4) 10.31159 -1.20121 0.58755 10.49251 -1.37922 1.24552
+CYS( 5) 12.70448 -3.80621 -0.72715 12.00677 -4.42453 -1.62291
+ALA( 6) 16.44175 -4.52019 -0.93521 16.93092 -4.21944 -0.52386
+ALA( 7) 15.86025 -8.21957 -0.36540 15.35081 -8.39881 0.18621
+ALA( 8) 14.54201 -10.62082 -2.95704 15.23594 -10.34816 -3.30696
+ALA( 9) 13.65028 -14.25975 -2.52064 13.75752 -14.37646 -1.85337
+ALA( 10) 9.97261 -13.41422 -2.44808 9.57534 -12.87986 -2.05316
+ALA( 11) 8.11976 -14.33184 -5.57450 7.45061 -14.36484 -5.75243
+ALA( 12) 8.22776 -10.70552 -6.66675 7.55286 -10.55609 -6.40015
+ALA( 13) 10.03788 -7.45810 -7.66343 10.00976 -7.43698 -8.41753
+CYS( 14) 9.73131 -4.07719 -5.85807 9.66544 -4.28710 -4.56332
+ALA( 15) 11.05109 -0.55921 -6.62480 11.07862 0.01250 -7.09856
+ALA( 16) 10.83158 2.44432 -4.15315 11.20676 2.82955 -3.60782
+ALA( 17) 10.22466 6.01060 -5.34864 10.29490 6.35777 -5.85338
+GLY( 18) 6.77188 7.36501 -4.73819 6.77188 7.36501 -4.73819
+
+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 3.798 0.000 0.000 0.812 126.829 -76.902
+ALA 3 3.737 142.050 0.000 0.749 137.463 -84.306
+ALA 4 3.777 124.464 -169.125 0.705 105.294 -78.108
+CYS 5 3.774 110.120 -160.528 1.293 158.619 -104.565
+ALA 6 3.811 140.379 -177.281 0.706 135.838 -82.329
+ALA 7 3.788 91.388 142.499 0.772 126.337 -76.931
+ALA 8 3.771 124.902 75.891 0.824 113.900 -118.360
+ALA 9 3.772 128.130 -174.931 0.686 107.064 -87.141
+ALA 10 3.774 90.943 102.826 0.774 157.826 -59.303
+ALA 11 3.748 114.254 105.902 0.693 119.632 -54.909
+ALA 12 3.789 89.544 -101.667 0.741 155.157 -110.619
+ALA 13 3.849 153.580 60.970 0.755 140.632 -99.009
+CYS 14 3.845 125.646 -120.233 1.313 150.049 -92.166
+ALA 15 3.835 133.262 -173.688 0.743 134.737 -34.633
+ALA 16 3.896 124.125 -171.229 0.766 131.592 -41.437
+ALA 17 3.810 122.109 -144.160 0.617 138.711 -49.120
+GLY 18 3.759 115.636 105.386 0.000 180.000 180.000
+ Potential energy and its components
+
+Virtual-chain energies:
+
+EVDW= -2.922994E+01 WEIGHT= 1.352790E+00 (SC-SC)
+EVDW2= 1.284609E+01 WEIGHT= 1.593040E+00 (SC-p)
+EES= -1.045287E+01 WEIGHT= 7.153400E-01 (p-p)
+EVDWPP= -2.004779E+01 WEIGHT= 1.137100E-01 (p-p VDW)
+ESTR= 1.857136E+01 WEIGHT= 1.000000E+00 (stretching)
+EBE= -1.634855E+01 WEIGHT= 1.138730E+00 (bending)
+ESC= 5.355337E+01 WEIGHT= 1.625800E-01 (SC local)
+ETORS= 8.666828E+00 WEIGHT= 1.985990E+00 (torsional)
+ETORSD= -6.630800E-01 WEIGHT= 1.570690E+00 (double torsional)
+EHPB= -1.208519E+01 WEIGHT= 1.000000E+00 (SS bridges & dist. cnstr.)
+ECORR4= -8.168927E+00 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= 1.099339E+01 WEIGHT= 1.603600E-01 (electrostatic-local)
+ETURN3= 4.828306E+00 WEIGHT= 1.687220E+00 (turns, 3rd order)
+ETURN4= 7.195922E+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= -5.500000E+00 (disulfide-bridge intrinsic energy)
+UCONST= 0.000000E+00 (Constraint energy)
+ETOT= -4.915833E+00 (total)
+
+Initial:
+ Kinetic energy 3.03426E+01
+ potential energy -4.91583E+00
+ total energy 2.54268E+01
+
+ maximum acceleration 2.53291E+00
+
+
+
+=================================== Timing ===================================
+
+ MD calculations setup: 1.17188E-02
+ Energy & gradient evaluation: 1.13281E-01
+ Stochastic MD setup: 0.00000E+00
+ Stochastic MD step setup: 0.00000E+00
+ MD steps: 1.30078E+00
+
+
+============================ End of MD calculation ===========================
+CG processor 0 is finishing work.
+ Total wall clock time 1.33984375000000 sec
projects / unres.git / blobdiff