--- /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 30
+ compiled Wed Nov 7 12:05:42 2012
+ 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: 20000
+ 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: 1000
+ Frequency of coordinate output: 300
+Berendsen bath calculation
+ Temperature: 400.00000
+ Coupling constant (tau): 1.00000
+Momenta will be reset at zero every 1000 steps
+
+============================== End of MD run setup =============================
+
+
+Energy-term weights (unscaled):
+
+WSCC= 1.000000 (SC-SC)
+WSCP= 2.794050 (SC-p)
+WELEC= 0.145810 (p-p electr)
+WVDWPP= 0.145810 (p-p VDW)
+WBOND= 1.000000 (stretching)
+WANG= 1.956840 (bending)
+WSCLOC= 0.170100 (SC local)
+WTOR= 2.046980 (torsional)
+WTORD= 1.696240 (double torsional)
+WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
+WEL_LOC= 1.218370 (multi-body 3-rd order)
+WCORR4= 1.846150 (multi-body 4th order)
+WCORR5= 0.027300 (multi-body 5th order)
+WCORR6= 0.007410 (multi-body 6th order)
+WSCCOR= 1.000000 (back-scloc correlation)
+WTURN3= 2.913860 (turns, 3rd order)
+WTURN4= 0.731780 (turns, 4th order)
+WTURN6= 0.023910 (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= 2.794050 (SC-p)
+WELEC= 0.117327 (p-p electr)
+WVDWPP= 0.145810 (p-p VDW)
+WBOND= 1.000000 (stretching)
+WANG= 1.956840 (bending)
+WSCLOC= 0.170100 (SC local)
+WTOR= 1.647115 (torsional)
+WTORD= 1.058472 (double torsional)
+WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
+WEL_LOC= 0.760276 (multi-body 3-rd order)
+WCORR4= 0.874494 (multi-body 4th order)
+WCORR5= 0.009729 (multi-body 5th order)
+WCORR6= 0.001982 (multi-body 6th order)
+WSCCOR= 0.804656 (back-scloc correlatkion)
+WTURN3= 1.818280 (turns, 3rd order)
+WTURN4= 0.346633 (turns, 4th order)
+WTURN6= 0.006394 (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 -6.90133843152500
+ HT -1.40133843152500
+ 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
+Initial geometry will be read in.
+
+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 3.800 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
+CYS 5 3.800 90.000 180.000 1.237 100.000 -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
+ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000
+ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000
+CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000
+ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000
+ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000
+ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000
+GLY 18 3.800 90.000 180.000 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 0.39133 0.02679 0.27319 0.00000 0.00000 0.00000
+ 1 -0.17409 -0.26585 -0.21721 0.00000 0.00000 0.00000
+ 2 -0.17148 0.42025 0.20576 -0.07613 0.16475 0.01193
+ 3 -0.01404 -0.36110 -0.46494 -0.31406 0.04480 -0.30309
+ 4 0.15172 0.29663 0.29266 -0.07974 0.11323 0.22586
+ 5 -0.32168 -0.01456 0.05151 -0.17812 -0.01530 -0.02557
+ 6 0.11448 0.13832 0.17223 -0.12900 -0.20376 -0.11786
+ 7 -0.18175 -0.37828 -0.09633 -0.17966 -0.19816 -0.31341
+ 8 -0.02028 0.22735 -0.36928 -0.04858 0.08355 -0.26764
+ 9 0.34459 -0.25203 0.14694 0.01426 -0.12058 -0.21343
+ 10 -0.41200 0.20762 -0.12944 -0.00588 -0.02316 0.01848
+ 11 0.48857 -0.08617 0.25832 0.35227 -0.04402 0.04919
+ 12 -0.32840 -0.19630 -0.27333 -0.07994 -0.13029 -0.14699
+ 13 0.13872 0.24955 0.17068 0.08823 0.11539 0.21615
+ 14 0.18253 0.02951 -0.14956 -0.11740 -0.10145 -0.17371
+ 15 -0.19102 -0.09980 0.23974 0.03607 -0.01130 0.14715
+ 16 0.08092 0.16784 -0.32778 0.01162 0.30480 -0.18318
+ 17 -0.14311 -0.25973 0.34658 -0.44245 -0.17578 0.34891
+ 18 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
+ Calling the zero-angular momentum subroutine
+ vcm right after adjustment:
+ 2.064717366521174E-017 -1.189837126469829E-017 5.249281440308069E-018
+
+
+ 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) 3.80000 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
+CYS( 5) 7.60000 -7.60000 0.00000 7.01741 -7.32119 -1.05500
+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
+ALA( 12) 22.80000 -19.00000 0.00000 22.73284 -18.57346 0.60465
+ALA( 13) 22.80000 -22.80000 0.00000 22.45007 -22.63253 -0.63368
+CYS( 14) 26.60000 -22.80000 0.00000 26.48819 -22.08987 1.00667
+ALA( 15) 26.60000 -26.60000 0.00000 26.25007 -26.43253 -0.63368
+ALA( 16) 30.40000 -26.60000 0.00000 30.33284 -26.17346 0.60465
+ALA( 17) 30.40000 -30.40000 0.00000 29.97346 -30.33284 -0.60465
+GLY( 18) 34.20000 -30.40000 0.00000 34.20000 -30.40000 0.00000
+
+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 3.800 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
+CYS 5 3.800 90.000 180.000 1.237 100.000 -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
+ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000
+ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000
+CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000
+ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000
+ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000
+ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000
+GLY 18 3.800 90.000 180.000 0.000 180.000 180.000
+ Potential energy and its components
+
+Virtual-chain energies:
+
+EVDW= -1.784028E+01 WEIGHT= 1.000000D+00 (SC-SC)
+EVDW2= 2.118779E+01 WEIGHT= 2.794050D+00 (SC-p)
+EES= -8.122745E+00 WEIGHT= 1.173269D-01 (p-p)
+EVDWPP= -2.540621E+01 WEIGHT= 1.458100D-01 (p-p VDW)
+ESTR= 4.237046E-27 WEIGHT= 1.000000D+00 (stretching)
+EBE= -1.185178E+00 WEIGHT= 1.956840D+00 (bending)
+ESC= 1.520408E+02 WEIGHT= 1.701000D-01 (SC local)
+ETORS= 0.000000E+00 WEIGHT= 1.647115D+00 (torsional)
+ETORSD= -2.194244E+00 WEIGHT= 1.058472D+00 (double torsional)
+EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4= -5.324225E+00 WEIGHT= 8.744941D-01 (multi-body)
+ECORR5= 2.317900E+01 WEIGHT= 9.728750D-03 (multi-body)
+ECORR6= 1.215220E+01 WEIGHT= 1.981519D-03 (multi-body)
+EELLO= 3.759544E+01 WEIGHT= 7.602761D-01 (electrostatic-local)
+ETURN3= -3.193381E+00 WEIGHT= 1.818280D+00 (turns, 3rd order)
+ETURN4= 1.424793E+01 WEIGHT= 3.466334D-01 (turns, 4th order)
+ETURN6= 0.000000E+00 WEIGHT= 6.393807D-03 (turns, 6th order)
+ESCCOR= 7.779132E+00 WEIGHT= 8.046559D-01 (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= 8.749073E+01 (total)
+
+Initial:
+ Kinetic energy 3.88148E+01
+ potential energy 8.74907E+01
+ total energy 1.26306E+02
+
+ maximum acceleration 4.30400E+00
+
+Momenta zeroed out, time 78.83
+Momenta zeroed out, time 165.42
+Momenta zeroed out, time 241.14
+Momenta zeroed out, time 327.40
+Momenta zeroed out, time 415.61
+Momenta zeroed out, time 493.13
+Momenta zeroed out, time 570.53
+Momenta zeroed out, time 657.29
+Momenta zeroed out, time 739.56
+Momenta zeroed out, time 822.78
+Momenta zeroed out, time 908.08
+Momenta zeroed out, time 989.26
+Momenta zeroed out, time 1059.64
+Momenta zeroed out, time 1147.47
+Momenta zeroed out, time 1226.41
+Momenta zeroed out, time 1311.13
+Momenta zeroed out, time 1399.66
+Momenta zeroed out, time 1479.65
+Momenta zeroed out, time 1556.70
+Momenta zeroed out, time 1642.45
+
+
+=================================== Timing ===================================
+
+ MD calculations setup: 8.20312E-02
+ Energy & gradient evaluation: 8.30078E+00
+ Stochastic MD setup: 0.00000E+00
+ Stochastic MD step setup: 0.00000E+00
+ MD steps: 1.05234E+01
+
+
+============================ End of MD calculation ===========================
+CG processor 0 is finishing work.
+ Total wall clock time 10.9140625000000 sec
projects / unres.git / blobdiff