--- /dev/null
+--------------------------------------------------------------------------------
+ FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file : small.inp
+ Output file : small.out_GB
+
+ 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
+--------------------------------------------------------------------------------
+ ### LAST MODIFIED 03/28/12 23:29 by czarek
+ ++++ Compile info ++++
+ Version 3.1 build 27
+ compiled Fri Oct 5 13:10:24 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:
+ 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: 50000
+ 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 0.000000000000000E+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
+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
+
+Pre-formed links are:
+
+CYS( 5) -- CYS( 14) 0.000 -5.500 0.000
+
+Mesoscopic molecular dynamics (MD) calculation.
+
+********************************************************************************
+
+ Calling chainbuild
+====================MD calculation start====================
+ Initial velocities randomly generated
+ Initial velocities
+ 0 -0.33453 -0.07483 -0.03206 0.00000 0.00000 0.00000
+ 1 0.60801 0.09078 -0.01649 0.00000 0.00000 0.00000
+ 2 -0.22717 -0.43486 0.29485 0.06489 -0.21337 0.35299
+ 3 0.15327 0.53566 -0.23305 -0.24688 -0.00986 -0.12275
+ 4 0.06228 -0.05375 0.06294 -0.19345 0.02670 0.20836
+ 5 -0.33309 0.05139 -0.01429 -0.12351 -0.00675 -0.09273
+ 6 -0.06817 -0.22870 -0.04737 0.20671 -0.13568 -0.21386
+ 7 0.50143 0.23749 0.03096 -0.16319 0.01175 -0.03820
+ 8 -0.13754 0.04563 0.12172 -0.02843 -0.01504 -0.10702
+ 9 -0.11966 -0.06273 0.01098 -0.25787 -0.12974 -0.03183
+ 10 -0.29196 -0.21182 -0.28091 -0.13032 -0.00023 -0.02943
+ 11 0.17078 0.30325 0.24474 0.21168 -0.19118 0.08836
+ 12 -0.02379 -0.04666 -0.03493 0.00932 -0.18572 -0.02650
+ 13 0.26454 -0.06093 -0.40002 0.19547 -0.19792 0.00495
+ 14 -0.36457 -0.27710 0.61404 -0.15632 0.07442 0.10234
+ 15 0.14723 0.29638 -0.15981 0.45708 -0.09130 0.03430
+ 16 -0.02356 0.03470 -0.42550 0.09899 -0.15554 -0.09256
+ 17 0.09038 -0.11432 0.34794 -0.14072 0.01732 0.14744
+ 18 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
+ Calling the zero-angular momentum subroutine
+ vcm right after adjustment:
+ 1.312320360077017E-019 2.014411752718222E-017 -9.448706592554524E-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= -1.784016E+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= 0.000000E+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= -5.500000E+00 (disulfide-bridge intrinsic energy)
+UCONST= 0.000000E+00 (Constraint energy)
+ETOT= 8.664685E+01 (total)
+
+Initial:
+ Kinetic energy 4.43916E+01
+ potential energy 8.66468E+01
+ total energy 1.31038E+02
+
+ maximum acceleration 4.30607E+00
+
+Momenta zeroed out, time 82.24
+Momenta zeroed out, time 167.24
+Momenta zeroed out, time 256.61
+Momenta zeroed out, time 336.19
+Momenta zeroed out, time 424.42
+Momenta zeroed out, time 501.35
+Momenta zeroed out, time 594.96
+Momenta zeroed out, time 676.75
+Momenta zeroed out, time 763.06
+Momenta zeroed out, time 852.52
+Momenta zeroed out, time 929.93
+Momenta zeroed out, time 1011.97
+Momenta zeroed out, time 1086.41
+Momenta zeroed out, time 1172.78
+Momenta zeroed out, time 1244.29
+Momenta zeroed out, time 1327.03
+Momenta zeroed out, time 1414.35
+Momenta zeroed out, time 1505.75
+Momenta zeroed out, time 1588.07
+Momenta zeroed out, time 1682.50
+Momenta zeroed out, time 1761.66
+Momenta zeroed out, time 1842.58
+Momenta zeroed out, time 1924.54
+Momenta zeroed out, time 2006.16
+Momenta zeroed out, time 2095.77
+Momenta zeroed out, time 2174.07
+Momenta zeroed out, time 2250.48
+Momenta zeroed out, time 2327.93
+Momenta zeroed out, time 2415.08
+Momenta zeroed out, time 2484.46
+Momenta zeroed out, time 2553.97
+Momenta zeroed out, time 2639.64
+Momenta zeroed out, time 2715.89
+Momenta zeroed out, time 2803.24
+Momenta zeroed out, time 2888.74
+Momenta zeroed out, time 2967.55
+Momenta zeroed out, time 3050.82
+Momenta zeroed out, time 3139.25
+Momenta zeroed out, time 3220.06
+Momenta zeroed out, time 3310.99
+Momenta zeroed out, time 3386.65
+Momenta zeroed out, time 3462.21
+Momenta zeroed out, time 3542.12
+Momenta zeroed out, time 3625.49
+Momenta zeroed out, time 3713.61
+Momenta zeroed out, time 3793.08
+Momenta zeroed out, time 3876.16
+Momenta zeroed out, time 3955.62
+Momenta zeroed out, time 4032.18
+Momenta zeroed out, time 4113.16
+
+
+=================================== Timing ===================================
+
+ MD calculations setup: 1.00000E-02
+ Energy & gradient evaluation: 2.00600E+01
+ Stochastic MD setup: 0.00000E+00
+ Stochastic MD step setup: 0.00000E+00
+ MD steps: 2.10900E+01
+
+
+============================ End of MD calculation ===========================
+
+
+***** Computation time: 0 hours 0 minutes 21 seconds *****
projects / unres.git / blobdiff