+++ /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