+++ /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