+++ /dev/null
---------------------------------------------------------------------------------
- FILE ASSIGNMENT
---------------------------------------------------------------------------------
- Input file : 1L2Y_REMD.inp
- Output file : 1L2Y_REMD.out_GB000
-
- Sidechain potential file :
- /users/pk376/unres-git/unres/PARAM/scinter_GB.parm
- SCp potential file : /users/pk376/unres-git/unres/PARAM/scp.parm
- Electrostatic potential file :
- /users/pk376/unres-git/unres/PARAM/electr_631Gdp.parm
- Cumulant coefficient file :
- /users/pk376/unres-git/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3
- Torsional parameter file :
- /users/pk376/unres-git/unres/PARAM/torsion_631Gdp.parm
- Double torsional parameter file :
- /users/pk376/unres-git/unres/PARAM/torsion_double_631Gdp.parm
- SCCOR parameter file : /users/pk376/unres-git/unres/PARAM/sccor_pdb_shelly.dat
- Bond & inertia constant file :
- /users/pk376/unres-git/unres/PARAM/bond_AM1.parm
- Bending parameter file :
- /users/pk376/unres-git/unres/PARAM/theta_abinitio.parm
- Rotamer parameter file :
- /users/pk376/unres-git/unres/PARAM/rotamers_AM1_aura.10022007.parm
- Threading database :
- /users/pk376/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 2.5 build 303
- compiled Mon Jul 23 17:44:56 2012
- compiled by jal47@matrix.chem.cornell.edu
- OS name: Linux
- OS release: 2.6.34.9-69.fc13.x86_64
- OS version: #1 SMP Tue May 3 09:23:03 UTC 2011
- flags:
- INSTALL_DIR = /users/software/mpich-1.2.7p1_int...
- FC= ifort
- OPT = -g -ip -w -CB
- 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 ++++
- Start reading THETA_PDB
- End reading THETA_PDB
-
-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 -46
- -45086
- 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: 1000000
- Initial time step of numerical integration: 0.20000 natural units
- 9.78000 fs
-A-MTS algorithm used; initial time step for fast-varying short-range forces split into 1 steps.
-Short-range force cutoff 2.00 lambda 0.30
-Maximum acceleration threshold to reduce the time step/increase split number: 10.00000
-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: 10000
- Frequency of coordinate output: 10000
-Berendsen bath calculation
- Temperature: 300.00000
- Coupling constant (tau): 1.00000
-Momenta will be reset at zero every 1000 steps
-Velocities will be reset at random every 10000 steps
-
-============================== End of MD run setup =============================
-
- REMD setup
- NREP= 16
- NSTEX= 100000
- SYNC= T
- NSYN= 100000
- TRAJCACHE= 1
- tlist 250.000000000000 260.000000000000 270.000000000000
- 280.000000000000 290.000000000000 300.000000000000
- 310.000000000000 320.000000000000 330.000000000000
- 340.000000000000 350.000000000000 360.000000000000
- 370.000000000000 380.000000000000 390.000000000000
- 400.000000000000
- mlist 1 1 1 1 1 1
- 1 1 1 1 1 1
- 1 1 1 1
- Total number of replicas 16
-
-============================== End of REMD run setup =============================
-
-
-Energy-term weights (unscaled):
-
-WSCC= 1.000000 (SC-SC)
-WSCP= 1.233150 (SC-p)
-WELEC= 0.844760 (p-p electr)
-WVDWPP= 0.231730 (p-p VDW)
-WBOND= 1.000000 (stretching)
-WANG= 0.629540 (bending)
-WSCLOC= 0.105540 (SC local)
-WTOR= 1.843160 (torsional)
-WTORD= 1.265710 (double torsional)
-WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
-WEL_LOC= 0.373570 (multi-body 3-rd order)
-WCORR4= 0.192120 (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= 1.403230 (turns, 3rd order)
-WTURN4= 0.646730 (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= 1.000000 (SC-SC)
-WSCP= 1.233150 (SC-p)
-WELEC= 0.844760 (p-p electr)
-WVDWPP= 0.231730 (p-p VDW)
-WBOND= 1.000000 (stretching)
-WANG= 0.629540 (bending)
-WSCLOC= 0.105540 (SC local)
-WTOR= 1.843160 (torsional)
-WTORD= 1.265710 (double torsional)
-WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
-WEL_LOC= 0.373570 (multi-body 3-rd order)
-WCORR4= 0.192120 (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= 1.403230 (turns, 3rd order)
-WTURN4= 0.646730 (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
-PDB data will be read from file ../../../../1L2Y.pdb
- Nres: 21
-Backbone and SC coordinates as read from the PDB
- 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
- 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
- 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
- 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
- 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
- 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
- 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
- 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
- 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
- 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
- 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
- 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
- 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
- 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
- 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
- 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
- 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
- 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
- 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
- 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
- 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
- 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
-nsup= 20 nstart_sup= 2
- ITEL
- 1 21 0
- 2 14 1
- 3 5 1
- 4 8 1
- 5 4 1
- 6 13 1
- 7 7 1
- 8 5 1
- 9 19 1
- 10 16 1
- 11 10 1
- 12 10 2
- 13 20 1
- 14 12 1
- 15 12 1
- 16 10 1
- 17 18 2
- 18 20 2
- 19 20 2
- 20 20 1
- 21 12 0
- ns= 0 iss:
-Boundaries in phi angle sampling:
-D 1 -180.0 180.0
-ASN 2 -180.0 180.0
-LEU 3 -180.0 180.0
-TYR 4 -180.0 180.0
-ILE 5 -180.0 180.0
-GLN 6 -180.0 180.0
-TRP 7 -180.0 180.0
-LEU 8 -180.0 180.0
-LYS 9 -180.0 180.0
-ASP 10 -180.0 180.0
-GLY 11 -180.0 180.0
-GLY 12 -180.0 180.0
-PRO 13 -180.0 180.0
-SER 14 -180.0 180.0
-SER 15 -180.0 180.0
-GLY 16 -180.0 180.0
-ARG 17 -180.0 180.0
-PRO 18 -180.0 180.0
-PRO 19 -180.0 180.0
-PRO 20 -180.0 180.0
-SER 21 -180.0 180.0
-D 22 -180.0 180.0
-nsup= 20
- nsup= 20 nstart_sup= 2 nstart_seq= 2
- NZ_START= 2 NZ_END= 21
- IZ_SC= 0
- Contact order: 0.308441558441558
- Shifting contacts: 2 2
- 1 ILE 5 ASN 2
- 2 TRP 7 TYR 4
- 3 LEU 8 TYR 4
- 4 LEU 8 ILE 5
- 5 LYS 9 GLN 6
- 6 GLY 12 TRP 7
- 7 GLY 12 LEU 8
- 8 SER 14 GLY 11
- 9 SER 15 ASP 10
- 10 SER 15 GLY 11
- 11 PRO 19 TRP 7
- 12 PRO 20 LEU 3
- 13 PRO 20 TYR 4
- 14 PRO 20 TRP 7
- j 2 k 3
-+dist.constr 1 2 3 3.88 3.70E-02
- j 2 k 4
-+dist.constr 2 2 4 5.58 2.68E-02
- j 2 k 5
-+dist.constr 3 2 5 5.04 3.01E-02
- j 2 k 6
-+dist.constr 4 2 6 6.32 2.25E-02
- j 2 k 7
-+dist.constr 5 2 7 8.77 1.07E-02
- j 2 k 8
-+dist.constr 6 2 8 9.91 7.02E-03
- j 2 k 9
-+dist.constr 7 2 9 10.61 5.25E-03
- j 2 k 10
-+dist.constr 8 2 10 12.89 1.80E-03
- j 3 k 4
-+dist.constr 9 3 4 3.86 3.71E-02
- j 3 k 5
-+dist.constr 10 3 5 5.48 2.74E-02
- j 3 k 6
-+dist.constr 11 3 6 5.24 2.89E-02
- j 3 k 7
-+dist.constr 12 3 7 6.43 2.19E-02
- j 3 k 8
-+dist.constr 13 3 8 8.85 1.04E-02
- j 3 k 9
-+dist.constr 14 3 9 10.21 6.21E-03
- j 3 k 10
-+dist.constr 15 3 10 11.39 3.74E-03
- j 4 k 5
-+dist.constr 16 4 5 3.87 3.70E-02
- j 4 k 6
-+dist.constr 17 4 6 5.41 2.78E-02
- j 4 k 7
-+dist.constr 18 4 7 4.91 3.09E-02
- j 4 k 8
-+dist.constr 19 4 8 6.11 2.37E-02
- j 4 k 9
-+dist.constr 20 4 9 8.65 1.12E-02
- j 4 k 10
-+dist.constr 21 4 10 10.11 6.47E-03
- j 5 k 6
-+dist.constr 22 5 6 3.85 3.72E-02
- j 5 k 7
-+dist.constr 23 5 7 5.39 2.80E-02
- j 5 k 8
-+dist.constr 24 5 8 5.08 2.99E-02
- j 5 k 9
-+dist.constr 25 5 9 6.11 2.37E-02
- j 5 k 10
-+dist.constr 26 5 10 8.79 1.07E-02
- j 6 k 7
-+dist.constr 27 6 7 3.87 3.71E-02
- j 6 k 8
-+dist.constr 28 6 8 5.61 2.67E-02
- j 6 k 9
-+dist.constr 29 6 9 5.36 2.82E-02
- j 6 k 10
-+dist.constr 30 6 10 6.73 2.02E-02
- j 7 k 8
-+dist.constr 31 7 8 3.86 3.71E-02
- j 7 k 9
-+dist.constr 32 7 9 5.70 2.61E-02
- j 7 k 10
-+dist.constr 33 7 10 5.59 2.68E-02
- j 8 k 9
-+dist.constr 34 8 9 3.88 3.70E-02
- j 8 k 10
-+dist.constr 35 8 10 5.38 2.80E-02
- j 9 k 10
-+dist.constr 36 9 10 3.86 3.71E-02
-+dist.constr 1 2 3 3.88 0.00 0 0.0
-+dist.constr 2 2 4 5.58 0.00 0 0.0
-+dist.constr 3 2 5 5.04 0.00 0 0.0
-+dist.constr 4 2 6 6.32 0.00 0 0.0
-+dist.constr 5 2 7 8.77 0.00 0 0.0
-+dist.constr 6 2 8 9.91 0.00 0 0.0
-+dist.constr 7 2 9 10.61 0.00 0 0.0
-+dist.constr 8 2 10 12.89 0.00 0 0.0
-+dist.constr 9 3 4 3.86 0.00 0 0.0
-+dist.constr 10 3 5 5.48 0.00 0 0.0
-+dist.constr 11 3 6 5.24 0.00 0 0.0
-+dist.constr 12 3 7 6.43 0.00 0 0.0
-+dist.constr 13 3 8 8.85 0.00 0 0.0
-+dist.constr 14 3 9 10.21 0.00 0 0.0
-+dist.constr 15 3 10 11.39 0.00 0 0.0
-+dist.constr 16 4 5 3.87 0.00 0 0.0
-+dist.constr 17 4 6 5.41 0.00 0 0.0
-+dist.constr 18 4 7 4.91 0.00 0 0.0
-+dist.constr 19 4 8 6.11 0.00 0 0.0
-+dist.constr 20 4 9 8.65 0.00 0 0.0
-+dist.constr 21 4 10 10.11 0.00 0 0.0
-+dist.constr 22 5 6 3.85 0.00 0 0.0
-+dist.constr 23 5 7 5.39 0.00 0 0.0
-+dist.constr 24 5 8 5.08 0.00 0 0.0
-+dist.constr 25 5 9 6.11 0.00 0 0.0
-+dist.constr 26 5 10 8.79 0.00 0 0.0
-+dist.constr 27 6 7 3.87 0.00 0 0.0
-+dist.constr 28 6 8 5.61 0.00 0 0.0
-+dist.constr 29 6 9 5.36 0.00 0 0.0
-+dist.constr 30 6 10 6.73 0.00 0 0.0
-+dist.constr 31 7 8 3.86 0.00 0 0.0
-+dist.constr 32 7 9 5.70 0.00 0 0.0
-+dist.constr 33 7 10 5.59 0.00 0 0.0
-+dist.constr 34 8 9 3.88 0.00 0 0.0
-+dist.constr 35 8 10 5.38 0.00 0 0.0
-+dist.constr 36 9 10 3.86 0.00 0 0.0
-
-Geometry of the virtual chain.
- Res d Theta Gamma Dsc Alpha Beta
-D 1 0.000 0.000 0.000 0.000 0.000 0.000
-ASN 2 3.861 0.000 0.000 1.977 94.624 -178.093
-LEU 3 3.876 92.239 0.000 2.195 102.878 -79.236
-TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440
-ILE 5 3.871 90.357 45.849 1.692 144.011 -104.516
-GLN 6 3.846 89.090 55.194 2.338 170.986 -139.318
-TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913
-LEU 8 3.859 93.032 48.298 2.105 151.723 -105.899
-LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960
-ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646
-GLY 11 3.891 89.908 56.679 0.000 0.000 0.000
-GLY 12 3.864 100.181 -87.304 0.000 0.000 0.000
-PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580
-SER 14 3.876 89.537 4.261 1.267 144.515 -129.218
-SER 15 3.875 91.815 66.108 1.262 161.047 -100.177
-GLY 16 3.866 101.784 70.140 0.000 0.000 0.000
-ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716
-PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024
-PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417
-PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207
-SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341
-D 22 3.858 114.201 180.000 0.000 0.000 0.000
-
-
-********************************************************************************
- Processor 0: end reading molecular data.
-********************************************************************************
-
-
-The following 36 distance constraints have been imposed
- 1 2 3 0 3.87640 0.00000 0.03702
- 2 2 4 0 5.57666 0.00000 0.02684
- 3 2 5 0 5.03889 0.00000 0.03009
- 4 2 6 0 6.31641 0.00000 0.02251
- 5 2 7 0 8.76681 0.00000 0.01075
- 6 2 8 0 9.90813 0.00000 0.00702
- 7 2 9 0 10.61482 0.00000 0.00525
- 8 2 10 0 12.89033 0.00000 0.00180
- 9 3 4 0 3.86050 0.00000 0.03711
- 10 3 5 0 5.48434 0.00000 0.02740
- 11 3 6 0 5.23878 0.00000 0.02888
- 12 3 7 0 6.42590 0.00000 0.02189
- 13 3 8 0 8.85122 0.00000 0.01043
- 14 3 9 0 10.21149 0.00000 0.00621
- 15 3 10 0 11.38863 0.00000 0.00374
- 16 4 5 0 3.87147 0.00000 0.03705
- 17 4 6 0 5.41330 0.00000 0.02783
- 18 4 7 0 4.90831 0.00000 0.03088
- 19 4 8 0 6.10832 0.00000 0.02371
- 20 4 9 0 8.64580 0.00000 0.01121
- 21 4 10 0 10.11108 0.00000 0.00647
- 22 5 6 0 3.84558 0.00000 0.03720
- 23 5 7 0 5.38909 0.00000 0.02797
- 24 5 8 0 5.07567 0.00000 0.02987
- 25 5 9 0 6.11071 0.00000 0.02369
- 26 5 10 0 8.79273 0.00000 0.01065
- 27 6 7 0 3.86660 0.00000 0.03708
- 28 6 8 0 5.60509 0.00000 0.02667
- 29 6 9 0 5.35795 0.00000 0.02816
- 30 6 10 0 6.72791 0.00000 0.02022
- 31 7 8 0 3.85852 0.00000 0.03712
- 32 7 9 0 5.69883 0.00000 0.02611
- 33 7 10 0 5.58812 0.00000 0.02678
- 34 8 9 0 3.88180 0.00000 0.03699
- 35 8 10 0 5.37698 0.00000 0.02804
- 36 9 10 0 3.86099 0.00000 0.03711
-Replica exchange molecular dynamics (REMD) calculation.
-
-********************************************************************************
-
- Calling chainbuild
- Calling REMD
- MREMD 16 time before 5.078125000000000E-002
- NREP= 16
- i2rep 1 2 3 4 5 6 7 8 9 10
- 11 12 13 14 15 16
- i2set 1 1 1 1 1 1 1 1 1 1
- 1 1 1 1 1 1
- i,j,il,il1,i_index(i,j,il,il1)
-ifirst 1
- nupa 1: 2
-ndowna 1:
- nupa 2: 3
-ndowna 2: 1
- nupa 3: 4
-ndowna 3: 2
- nupa 4: 5
-ndowna 4: 3
- nupa 5: 6
-ndowna 5: 4
- nupa 6: 7
-ndowna 6: 5
- nupa 7: 8
-ndowna 7: 6
- nupa 8: 9
-ndowna 8: 7
- nupa 9: 10
-ndowna 9: 8
- nupa 10: 11
-ndowna 10: 9
- nupa 11: 12
-ndowna 11: 10
- nupa 12: 13
-ndowna 12: 11
- nupa 13: 14
-ndowna 13: 12
- nupa 14: 15
-ndowna 14: 13
- nupa 15: 16
-ndowna 15: 14
- nupa 16:
-ndowna 16: 15
- REMD Temperature: 250.00000
-====================MD calculation start====================
- Initial velocities randomly generated
- Initial velocities
- 0 0.02069 0.05735 -0.16550 0.00000 0.00000 0.00000
- 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
- 2 -0.32876 -0.20726 -0.00156 -0.06303 -0.02233 0.22619
- 3 0.25246 0.18847 0.12917 0.23917 0.13789 0.08528
- 4 0.09890 -0.10900 0.13430 0.09430 -0.08759 0.02991
- 5 0.05293 -0.08192 0.07599 0.03541 0.02418 -0.13426
- 6 0.01106 0.15012 -0.13429 -0.01486 0.10588 -0.15072
- 7 -0.00922 -0.05032 0.03343 -0.17306 0.05869 0.04136
- 8 -0.01642 0.12268 -0.04117 0.02116 0.09728 0.03398
- 9 -0.24153 -0.01761 0.08700 -0.20570 -0.15587 -0.04194
- 10 0.12837 -0.05524 -0.16763 0.18636 -0.14195 -0.15819
- 11 -0.12912 0.12012 -0.00669 0.00000 0.00000 0.00000
- 12 0.18024 -0.22147 0.01606 0.00000 0.00000 0.00000
- 13 -0.13972 0.25567 0.06619 0.05987 0.13532 0.09181
- 14 0.10136 -0.29158 0.14318 -0.02692 -0.08844 0.04927
- 15 0.13268 0.09441 -0.21684 -0.12710 0.07259 0.06988
- 16 -0.10926 0.13472 0.13695 0.00000 0.00000 0.00000
- 17 -0.08222 -0.14474 -0.18471 -0.07262 -0.07774 -0.09353
- 18 0.22036 0.08274 0.12819 -0.01893 0.09330 0.04480
- 19 -0.13103 -0.06596 -0.26603 -0.11327 -0.06258 -0.02718
- 20 0.26050 0.08237 0.51647 0.02143 0.14877 0.17591
- 21 0.00000 0.00000 0.00000 -0.12529 -0.05874 -0.20044
- 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
- Calling the zero-angular momentum subroutine
- vcm right after adjustment:
- 2.021371575869251E-017 -1.735521049988750E-018 1.041312629993250E-017
-
-
- alpha-carbon coordinates centroid coordinates
- X Y Z X Y Z
-D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
-ASN( 2) 3.86050 0.00000 0.00000 2.55159 1.47985 0.06557
-LEU( 3) 4.01193 -3.87344 0.00000 3.96088 -4.50305 -2.10206
-TYR( 4) 7.87243 -3.87344 0.00000 10.79652 -4.89021 -1.22632
-ILE( 5) 7.89655 -1.17680 2.77774 7.76075 0.44675 2.31935
-GLN( 6) 5.70141 -3.47509 4.94285 3.60888 -3.02771 5.88565
-TRP( 7) 8.16996 -6.36206 4.22016 10.77228 -8.29798 2.61912
-LEU( 8) 11.25658 -4.20989 5.07405 12.42370 -3.38205 3.52958
-LYS( 9) 9.76612 -2.79308 8.36640 6.86736 -2.82804 9.12493
-ASP( 10) 9.49962 -6.42561 9.64741 7.69328 -7.25489 9.53489
-GLY( 11) 13.31647 -6.90493 9.06335 13.31647 -6.90493 9.06335
-GLY( 12) 13.30671 -8.01769 5.36352 13.30671 -8.01769 5.36352
-PRO( 13) 15.31165 -11.32992 5.02827 16.17763 -10.48298 4.32295
-SER( 14) 15.75414 -11.41497 8.87760 16.77305 -10.71800 9.16233
-SER( 15) 11.95328 -11.92981 9.42670 11.12717 -10.97987 9.51528
-GLY( 16) 11.45094 -15.53878 8.13618 11.45094 -15.53878 8.13618
-ARG( 17) 9.54906 -14.31220 5.00147 7.79760 -12.40573 7.22288
-PRO( 18) 10.53690 -13.94710 1.26956 9.62009 -14.99504 1.15440
-PRO( 19) 10.30439 -10.55356 -0.55592 11.52337 -10.99526 -1.06954
-PRO( 20) 6.99735 -9.68439 -2.34313 7.03150 -8.66136 -1.39345
-SER( 21) 7.20688 -9.78655 -6.20031 7.28380 -10.16020 -6.79638
-D ( 22) 3.89984 -8.91739 -7.98752 3.89984 -8.91739 -7.98752
-
-Geometry of the virtual chain.
- Res d Theta Gamma Dsc Alpha Beta
-D 1 0.000 0.000 0.000 0.000 0.000 0.000
-ASN 2 3.861 0.000 0.000 1.977 94.624 -178.093
-LEU 3 3.876 92.239 0.000 2.195 102.878 -79.236
-TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440
-ILE 5 3.871 90.357 45.849 1.692 144.011 -104.516
-GLN 6 3.846 89.090 55.194 2.338 170.986 -139.318
-TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913
-LEU 8 3.859 93.032 48.298 2.105 151.723 -105.899
-LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960
-ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646
-GLY 11 3.891 89.908 56.679 0.000 180.000 180.000
-GLY 12 3.864 100.181 -87.304 0.000 180.000 180.000
-PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580
-SER 14 3.876 89.537 4.261 1.267 144.515 -129.218
-SER 15 3.875 91.815 66.108 1.262 161.047 -100.177
-GLY 16 3.866 101.784 70.140 0.000 180.000 180.000
-ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716
-PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024
-PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417
-PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207
-SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341
-D 22 3.858 114.201 180.000 0.000 180.000 180.000
- Potential energy and its components
-
-Virtual-chain energies:
-
-EVDW= -1.798849E+01 WEIGHT= 1.000000D+00 (SC-SC)
-EVDW2= 4.471415E+01 WEIGHT= 1.233150D+00 (SC-p)
-EES= -9.165378E+01 WEIGHT= 9.459849D-01 (p-p)
-EVDWPP= -3.362882E+01 WEIGHT= 2.317300D-01 (p-p VDW)
-ESTR= 5.659036E+01 WEIGHT= 1.000000D+00 (stretching)
-EBE= -5.669935E+00 WEIGHT= 6.295400D-01 (bending)
-ESC= 1.734458E+02 WEIGHT= 1.055400D-01 (SC local)
-ETORS= 1.479510E+01 WEIGHT= 2.064020D+00 (torsional)
-ETORSD= 1.006444E+00 WEIGHT= 1.555350D+00 (double torsional)
-EHPB= 2.258117E-31 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
-ECORR4= -6.528803E+01 WEIGHT= 2.541120D-01 (multi-body)
-ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
-ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
-EELLO= -4.012900E+00 WEIGHT= 4.590562D-01 (electrostatic-local)
-ETURN3= 1.829789E+01 WEIGHT= 1.724339D+00 (turns, 3rd order)
-ETURN4= 6.580750E-01 WEIGHT= 8.554124D-01 (turns, 4th order)
-ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
-ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+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= 5.976608E+01 (total)
-
-Initial:
- Kinetic energy 2.56370E+01
- potential energy 5.97661E+01
- total energy 8.54031E+01
-
- maximum acceleration 1.97137E+00
-
- Setup time 5.468750000000000E-002
-Velocities reset to random values, time 1999.80
-Velocities reset to random values, time 3999.80
-Velocities reset to random values, time 5999.80
-Velocities reset to random values, time 7999.80
-Velocities reset to random values, time 9999.80
-Velocities reset to random values, time 11999.80
-Velocities reset to random values, time 13999.80
-Velocities reset to random values, time 15999.80
-Velocities reset to random values, time 17999.80
-Velocities reset to random values, time 19999.80
- REMD synchro at 100000
- ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
- MIN ii_write= 1
- REMD gather times= 40.8046875000000 3.906250000000000E-003
- REMD writing rst time= 0.000000000000000E+000
- REMD writing traj time= 3.906250000000000E-003
- NREP 16
-ACC 1 250.00000 0.00000 1
-ACC 2 260.00000 1.00000 1
-ACC 3 270.00000 1.00000 1
-ACC 4 280.00000 0.00000 1
-ACC 5 290.00000 0.00000 1
-ACC 6 300.00000 1.00000 1
-ACC 7 310.00000 0.00000 1
-ACC 8 320.00000 1.00000 1
-ACC 9 330.00000 1.00000 1
-ACC 10 340.00000 1.00000 1
-ACC 11 350.00000 0.00000 1
-ACC 12 360.00000 1.00000 1
-ACC 13 370.00000 0.00000 1
-ACC 14 380.00000 1.00000 1
-ACC 15 390.00000 1.00000 1
- REMD scatter time= 0.000000000000000E+000
- REMD exchange time= 7.812500000000000E-003
-Velocities reset to random values, time 21999.80
-Velocities reset to random values, time 23999.80
-Velocities reset to random values, time 25999.80
-Velocities reset to random values, time 27999.80
-Velocities reset to random values, time 29999.80
-Velocities reset to random values, time 31999.80
-Velocities reset to random values, time 33999.80
-Velocities reset to random values, time 35999.80
-Velocities reset to random values, time 37999.80
-Velocities reset to random values, time 39999.80
- REMD synchro at 200000
- ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
- MIN ii_write= 1
- REMD gather times= 81.6015625000000 0.000000000000000E+000
- REMD writing rst time= 0.000000000000000E+000
- REMD writing traj time= 3.906250000000000E-003
- NREP 16
-ACC 1 250.00000 0.00000 2
-ACC 2 260.00000 0.50000 2
-ACC 3 270.00000 1.00000 2
-ACC 4 280.00000 0.50000 2
-ACC 5 290.00000 0.50000 2
-ACC 6 300.00000 1.00000 2
-ACC 7 310.00000 0.00000 2
-ACC 8 320.00000 0.50000 2
-ACC 9 330.00000 1.00000 2
-ACC 10 340.00000 1.00000 2
-ACC 11 350.00000 0.00000 2
-ACC 12 360.00000 1.00000 2
-ACC 13 370.00000 0.50000 2
-ACC 14 380.00000 1.00000 2
-ACC 15 390.00000 1.00000 2
- REMD scatter time= 0.000000000000000E+000
- REMD exchange time= 3.906250000000000E-003
-Velocities reset to random values, time 41999.80
-Velocities reset to random values, time 43999.80
-Velocities reset to random values, time 45999.80
-Velocities reset to random values, time 47999.80
-Velocities reset to random values, time 49999.80
-Velocities reset to random values, time 51999.80
-Velocities reset to random values, time 53999.80
-Velocities reset to random values, time 55999.80
-Velocities reset to random values, time 57999.80
-Velocities reset to random values, time 59999.80
- REMD synchro at 300000
- ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
- MIN ii_write= 1
- REMD gather times= 122.531250000000 0.000000000000000E+000
- REMD writing rst time= 3.906250000000000E-003
- REMD writing traj time= 3.906250000000000E-003
- NREP 16
-ACC 1 250.00000 0.33333 3
-ACC 2 260.00000 0.33333 3
-ACC 3 270.00000 1.00000 3
-ACC 4 280.00000 0.33333 3
-ACC 5 290.00000 0.66667 3
-ACC 6 300.00000 1.00000 3
-ACC 7 310.00000 0.00000 3
-ACC 8 320.00000 0.33333 3
-ACC 9 330.00000 1.00000 3
-ACC 10 340.00000 1.00000 3
-ACC 11 350.00000 0.33333 3
-ACC 12 360.00000 0.66667 3
-ACC 13 370.00000 0.66667 3
-ACC 14 380.00000 1.00000 3
-ACC 15 390.00000 1.00000 3
- REMD scatter time= 0.000000000000000E+000
- REMD exchange time= 7.812500000000000E-003
-Velocities reset to random values, time 61999.80
-Velocities reset to random values, time 63999.80
-Velocities reset to random values, time 65999.80
-Velocities reset to random values, time 67999.80
-Velocities reset to random values, time 69999.80
-Velocities reset to random values, time 71999.80
-Velocities reset to random values, time 73999.80
-Velocities reset to random values, time 75999.80
-Velocities reset to random values, time 77999.80
-Velocities reset to random values, time 79999.80
- REMD synchro at 400000
- ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
- MIN ii_write= 1
- REMD gather times= 163.546875000000 0.000000000000000E+000
- REMD writing rst time= 3.906250000000000E-003
- REMD writing traj time= 0.000000000000000E+000
- NREP 16
-ACC 1 250.00000 0.50000 4
-ACC 2 260.00000 0.25000 4
-ACC 3 270.00000 0.75000 4
-ACC 4 280.00000 0.25000 4
-ACC 5 290.00000 0.75000 4
-ACC 6 300.00000 0.75000 4
-ACC 7 310.00000 0.00000 4
-ACC 8 320.00000 0.50000 4
-ACC 9 330.00000 1.00000 4
-ACC 10 340.00000 1.00000 4
-ACC 11 350.00000 0.50000 4
-ACC 12 360.00000 0.75000 4
-ACC 13 370.00000 0.50000 4
-ACC 14 380.00000 1.00000 4
-ACC 15 390.00000 1.00000 4
- REMD scatter time= 0.000000000000000E+000
- REMD exchange time= 3.906250000000000E-003
-Velocities reset to random values, time 81999.80
-Velocities reset to random values, time 83999.80
-Velocities reset to random values, time 85999.80
-Velocities reset to random values, time 87999.80
-Velocities reset to random values, time 89999.80
-Velocities reset to random values, time 91999.80
-Velocities reset to random values, time 93999.80
-Velocities reset to random values, time 95999.80
-Velocities reset to random values, time 97999.80
-Velocities reset to random values, time 99999.80
- REMD synchro at 500000
- ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
- MIN ii_write= 1
- REMD gather times= 204.277343750000 0.000000000000000E+000
- REMD writing rst time= 0.000000000000000E+000
- REMD writing traj time= 3.906250000000000E-003
- NREP 16
-ACC 1 250.00000 0.40000 5
-ACC 2 260.00000 0.40000 5
-ACC 3 270.00000 0.80000 5
-ACC 4 280.00000 0.40000 5
-ACC 5 290.00000 0.80000 5
-ACC 6 300.00000 0.60000 5
-ACC 7 310.00000 0.00000 5
-ACC 8 320.00000 0.60000 5
-ACC 9 330.00000 1.00000 5
-ACC 10 340.00000 1.00000 5
-ACC 11 350.00000 0.60000 5
-ACC 12 360.00000 0.80000 5
-ACC 13 370.00000 0.60000 5
-ACC 14 380.00000 1.00000 5
-ACC 15 390.00000 1.00000 5
- REMD scatter time= 0.000000000000000E+000
- REMD exchange time= 3.906250000000000E-003
-Velocities reset to random values, time 101999.80
-Velocities reset to random values, time 103999.80
-Velocities reset to random values, time 105999.80
-Velocities reset to random values, time 107999.80
-Velocities reset to random values, time 109999.80
-Velocities reset to random values, time 111999.80
-Velocities reset to random values, time 113999.80
-Velocities reset to random values, time 115999.80
-Velocities reset to random values, time 117999.80
-Velocities reset to random values, time 119999.80
- REMD synchro at 600000
- ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
- MIN ii_write= 1
- REMD gather times= 245.050781250000 0.000000000000000E+000
- REMD writing rst time= 3.906250000000000E-003
- REMD writing traj time= 3.906250000000000E-003
- NREP 16
-ACC 1 250.00000 0.33333 6
-ACC 2 260.00000 0.50000 6
-ACC 3 270.00000 0.66667 6
-ACC 4 280.00000 0.50000 6
-ACC 5 290.00000 0.83333 6
-ACC 6 300.00000 0.50000 6
-ACC 7 310.00000 0.00000 6
-ACC 8 320.00000 0.66667 6
-ACC 9 330.00000 1.00000 6
-ACC 10 340.00000 0.83333 6
-ACC 11 350.00000 0.50000 6
-ACC 12 360.00000 0.83333 6
-ACC 13 370.00000 0.66667 6
-ACC 14 380.00000 1.00000 6
-ACC 15 390.00000 1.00000 6
- REMD scatter time= 0.000000000000000E+000
- REMD exchange time= 7.812500000000000E-003
-Velocities reset to random values, time 121999.80
-Velocities reset to random values, time 123999.80
-Velocities reset to random values, time 125999.80
-Velocities reset to random values, time 127999.80
-Velocities reset to random values, time 129999.80
-Velocities reset to random values, time 131999.80
-Velocities reset to random values, time 133999.80
-Velocities reset to random values, time 135999.80
-Velocities reset to random values, time 137999.80
-Velocities reset to random values, time 139999.80
- REMD synchro at 700000
- ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
- MIN ii_write= 1
- REMD gather times= 287.152343750000 0.000000000000000E+000
- REMD writing rst time= 0.000000000000000E+000
- REMD writing traj time= 7.812500000000000E-003
- NREP 16
-ACC 1 250.00000 0.28571 7
-ACC 2 260.00000 0.57143 7
-ACC 3 270.00000 0.71429 7
-ACC 4 280.00000 0.42857 7
-ACC 5 290.00000 0.85714 7
-ACC 6 300.00000 0.42857 7
-ACC 7 310.00000 0.14286 7
-ACC 8 320.00000 0.57143 7
-ACC 9 330.00000 1.00000 7
-ACC 10 340.00000 0.85714 7
-ACC 11 350.00000 0.57143 7
-ACC 12 360.00000 0.85714 7
-ACC 13 370.00000 0.57143 7
-ACC 14 380.00000 1.00000 7
-ACC 15 390.00000 0.85714 7
- REMD scatter time= 0.000000000000000E+000
- REMD exchange time= 7.812500000000000E-003
-Velocities reset to random values, time 141999.80
-Velocities reset to random values, time 143999.80
-Velocities reset to random values, time 145999.80
-Velocities reset to random values, time 147999.80
-Velocities reset to random values, time 149999.80
-Velocities reset to random values, time 151999.80
-Velocities reset to random values, time 153999.80
-Velocities reset to random values, time 155999.80
-Velocities reset to random values, time 157999.80
-Velocities reset to random values, time 159999.80
- REMD synchro at 800000
- ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
- MIN ii_write= 1
- REMD gather times= 328.453125000000 0.000000000000000E+000
- REMD writing rst time= 3.906250000000000E-003
- REMD writing traj time= 3.906250000000000E-003
- NREP 16
-ACC 1 250.00000 0.25000 8
-ACC 2 260.00000 0.50000 8
-ACC 3 270.00000 0.62500 8
-ACC 4 280.00000 0.37500 8
-ACC 5 290.00000 0.87500 8
-ACC 6 300.00000 0.37500 8
-ACC 7 310.00000 0.12500 8
-ACC 8 320.00000 0.62500 8
-ACC 9 330.00000 1.00000 8
-ACC 10 340.00000 0.87500 8
-ACC 11 350.00000 0.50000 8
-ACC 12 360.00000 0.87500 8
-ACC 13 370.00000 0.62500 8
-ACC 14 380.00000 0.87500 8
-ACC 15 390.00000 0.87500 8
- REMD scatter time= 0.000000000000000E+000
- REMD exchange time= 7.812500000000000E-003
-Velocities reset to random values, time 161999.80
-Velocities reset to random values, time 163999.80
-Velocities reset to random values, time 165999.80
-Velocities reset to random values, time 167999.80
-Velocities reset to random values, time 169999.80
-Velocities reset to random values, time 171999.80
-Velocities reset to random values, time 173999.80
-Velocities reset to random values, time 175999.80
-Velocities reset to random values, time 177999.80
-Velocities reset to random values, time 179999.80
- REMD synchro at 900000
- ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
- MIN ii_write= 1
- REMD gather times= 369.187500000000 0.000000000000000E+000
- REMD writing rst time= 3.906250000000000E-003
- REMD writing traj time= 0.000000000000000E+000
- NREP 16
-ACC 1 250.00000 0.33333 9
-ACC 2 260.00000 0.44444 9
-ACC 3 270.00000 0.66667 9
-ACC 4 280.00000 0.33333 9
-ACC 5 290.00000 0.88889 9
-ACC 6 300.00000 0.44444 9
-ACC 7 310.00000 0.11111 9
-ACC 8 320.00000 0.55556 9
-ACC 9 330.00000 1.00000 9
-ACC 10 340.00000 0.88889 9
-ACC 11 350.00000 0.44444 9
-ACC 12 360.00000 0.88889 9
-ACC 13 370.00000 0.55556 9
-ACC 14 380.00000 0.88889 9
-ACC 15 390.00000 0.88889 9
- REMD scatter time= 0.000000000000000E+000
- REMD exchange time= 3.906250000000000E-003
-Velocities reset to random values, time 181999.80
-Velocities reset to random values, time 183999.80
-Velocities reset to random values, time 185999.80
-Velocities reset to random values, time 187999.80
-Velocities reset to random values, time 189999.80
-Velocities reset to random values, time 191999.80
-Velocities reset to random values, time 193999.80
-Velocities reset to random values, time 195999.80
-Velocities reset to random values, time 197999.80
-Velocities reset to random values, time 199999.80
- REMD synchro at 1000000
- ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
- MIN ii_write= 1
- writing restart at the end of run
-
-
-=================================== Timing ===================================
-
- MD calculations setup: 3.90625E-03
- Energy & gradient evaluation: 3.76590E+02
- Stochastic MD setup: 0.00000E+00
- Stochastic MD step setup: 0.00000E+00
- MD steps: 4.10020E+02
-
-
-============================ End of MD calculation ===========================
-CG processor 0 is finishing work.
- Total wall clock time 410.074218750000 sec
projects / unres.git / blobdiff