--- /dev/null
+--------------------------------------------------------------------------------
+ FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file : 1L2Y_MREMD.inp
+ Output file : 1L2Y_MREMD.out_GB000
+
+ Sidechain potential file :
+ /users/czarek/UNRES/export_v3/PARAM/scinter_GB.parm
+ SCp potential file : /users/czarek/UNRES/export_v3/PARAM/scp.parm
+ Electrostatic potential file :
+ /users/czarek/UNRES/export_v3/PARAM/electr_631Gdp.parm
+ Cumulant coefficient file :
+ /users/czarek/UNRES/export_v3/PARAM/fourier_opt.parm.1igd_hc_iter3_3
+ Torsional parameter file :
+ /users/czarek/UNRES/export_v3/PARAM/torsion_631Gdp.parm
+ Double torsional parameter file :
+ /users/czarek/UNRES/export_v3/PARAM/torsion_double_631Gdp.parm
+ SCCOR parameter file : /users/czarek/UNRES/export_v3/PARAM/rotcorr_AM1.parm
+ Bond & inertia constant file : /users/czarek/UNRES/export_v3/PARAM/bond.parm
+ Bending parameter file :
+ /users/czarek/UNRES/export_v3/PARAM/thetaml.5parm
+ Rotamer parameter file :
+ /users/czarek/UNRES/export_v3/PARAM/scgauss.parm
+ Threading database :
+ /users/czarek/UNRES/export_v3/PARAM/patterns.cart
+--------------------------------------------------------------------------------
+********************************************************************************
+United-residue force field calculation - parallel job.
+********************************************************************************
+ ### LAST MODIFIED 04/08/11 11:00AM by czarek
+ ++++ Compile info ++++
+ Version 2.5 build 36
+ compiled Thu Dec 1 05:12:23 2011
+ compiled by czarek@matrix.chem.cornell.edu
+ OS name: Linux
+ OS release: 2.6.34.8-68.fc13.x86_64
+ OS version: #1 SMP Thu Feb 17 15:03:58 UTC 2011
+ flags:
+ CPPFLAGS = -DCRYST_BOND -DCRYST_THETA -DCRYST_S...
+ 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 ...
+ BIN = ../bin/unres_120111_mpich1_oldparm.exe
+ LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...
+ ARCH = LINUX
+ PP = /lib/cpp -P
+ object = unres.o arcos.o cartprint.o chainbuild...
+ ++++ 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= -3059742
+ ran_num 0.273754117333397
+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 4 4 4 4 4 4
+ 4 4 4 4 4 4
+ 4 4 4 4
+ Total number of replicas 64
+
+============================== End of REMD 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 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
+Extended chain initial geometry.
+
+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 3.800 0.000 0.000 1.684 110.000 -120.000
+LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
+TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
+ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
+GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
+TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
+LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
+LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
+ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
+GLY 11 3.800 90.000 180.000 0.000 110.000 -120.000
+GLY 12 3.800 90.000 180.000 0.000 110.000 -120.000
+PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
+SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
+SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
+GLY 16 3.800 90.000 180.000 0.000 110.000 -120.000
+ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
+PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
+PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
+PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
+SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
+D 22 3.800 90.000 180.000 0.000 0.000 0.000
+
+
+********************************************************************************
+ Processor 0: end reading molecular data.
+********************************************************************************
+
+
+Replica exchange molecular dynamics (REMD) calculation.
+
+********************************************************************************
+
+ Calling chainbuild
+ Calling REMD
+ MREMD 64 time before 0.558593750000000
+ NREP= 16
+ i2rep 1 1 1 1 2 2 2 2 3 3
+ 3 3 4 4 4 4 5 5 5 5 6
+ 6 6 6 7 7 7 7 8 8 8 8
+ 9 9 9 9 10 10 10 10 11 11 11
+ 11 12 12 12 12 13 13 13 13 14 14
+ 14 14 15 15 15 15 16 16 16 16
+ i2set 1 1 1 1 1 1 1 1 1 1
+ 1 1 1 1 1 1 1 1 1 1 1
+ 1 1 1 1 1 1 1 1 1 1 1
+ 1 1 1 1 1 1 1 1 1 1 1
+ 1 1 1 1 1 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 2 3 4
+ nupa 1: 5 6 7 8
+ndowna 1:
+ nupa 2: 5 6 7 8
+ndowna 2:
+ nupa 3: 5 6 7 8
+ndowna 3:
+ nupa 4: 5 6 7 8
+ndowna 4:
+ nupa 5: 9 10 11 12
+ndowna 5: 1 2 3 4
+ nupa 6: 9 10 11 12
+ndowna 6: 1 2 3 4
+ nupa 7: 9 10 11 12
+ndowna 7: 1 2 3 4
+ nupa 8: 9 10 11 12
+ndowna 8: 1 2 3 4
+ nupa 9: 13 14 15 16
+ndowna 9: 5 6 7 8
+ nupa 10: 13 14 15 16
+ndowna 10: 5 6 7 8
+ nupa 11: 13 14 15 16
+ndowna 11: 5 6 7 8
+ nupa 12: 13 14 15 16
+ndowna 12: 5 6 7 8
+ nupa 13: 17 18 19 20
+ndowna 13: 9 10 11 12
+ nupa 14: 17 18 19 20
+ndowna 14: 9 10 11 12
+ nupa 15: 17 18 19 20
+ndowna 15: 9 10 11 12
+ nupa 16: 17 18 19 20
+ndowna 16: 9 10 11 12
+ nupa 17: 21 22 23 24
+ndowna 17: 13 14 15 16
+ nupa 18: 21 22 23 24
+ndowna 18: 13 14 15 16
+ nupa 19: 21 22 23 24
+ndowna 19: 13 14 15 16
+ nupa 20: 21 22 23 24
+ndowna 20: 13 14 15 16
+ nupa 21: 25 26 27 28
+ndowna 21: 17 18 19 20
+ nupa 22: 25 26 27 28
+ndowna 22: 17 18 19 20
+ nupa 23: 25 26 27 28
+ndowna 23: 17 18 19 20
+ nupa 24: 25 26 27 28
+ndowna 24: 17 18 19 20
+ nupa 25: 29 30 31 32
+ndowna 25: 21 22 23 24
+ nupa 26: 29 30 31 32
+ndowna 26: 21 22 23 24
+ nupa 27: 29 30 31 32
+ndowna 27: 21 22 23 24
+ nupa 28: 29 30 31 32
+ndowna 28: 21 22 23 24
+ nupa 29: 33 34 35 36
+ndowna 29: 25 26 27 28
+ nupa 30: 33 34 35 36
+ndowna 30: 25 26 27 28
+ nupa 31: 33 34 35 36
+ndowna 31: 25 26 27 28
+ nupa 32: 33 34 35 36
+ndowna 32: 25 26 27 28
+ nupa 33: 37 38 39 40
+ndowna 33: 29 30 31 32
+ nupa 34: 37 38 39 40
+ndowna 34: 29 30 31 32
+ nupa 35: 37 38 39 40
+ndowna 35: 29 30 31 32
+ nupa 36: 37 38 39 40
+ndowna 36: 29 30 31 32
+ nupa 37: 41 42 43 44
+ndowna 37: 33 34 35 36
+ nupa 38: 41 42 43 44
+ndowna 38: 33 34 35 36
+ nupa 39: 41 42 43 44
+ndowna 39: 33 34 35 36
+ nupa 40: 41 42 43 44
+ndowna 40: 33 34 35 36
+ nupa 41: 45 46 47 48
+ndowna 41: 37 38 39 40
+ nupa 42: 45 46 47 48
+ndowna 42: 37 38 39 40
+ nupa 43: 45 46 47 48
+ndowna 43: 37 38 39 40
+ nupa 44: 45 46 47 48
+ndowna 44: 37 38 39 40
+ nupa 45: 49 50 51 52
+ndowna 45: 41 42 43 44
+ nupa 46: 49 50 51 52
+ndowna 46: 41 42 43 44
+ nupa 47: 49 50 51 52
+ndowna 47: 41 42 43 44
+ nupa 48: 49 50 51 52
+ndowna 48: 41 42 43 44
+ nupa 49: 53 54 55 56
+ndowna 49: 45 46 47 48
+ nupa 50: 53 54 55 56
+ndowna 50: 45 46 47 48
+ nupa 51: 53 54 55 56
+ndowna 51: 45 46 47 48
+ nupa 52: 53 54 55 56
+ndowna 52: 45 46 47 48
+ nupa 53: 57 58 59 60
+ndowna 53: 49 50 51 52
+ nupa 54: 57 58 59 60
+ndowna 54: 49 50 51 52
+ nupa 55: 57 58 59 60
+ndowna 55: 49 50 51 52
+ nupa 56: 57 58 59 60
+ndowna 56: 49 50 51 52
+ nupa 57: 61 62 63 64
+ndowna 57: 53 54 55 56
+ nupa 58: 61 62 63 64
+ndowna 58: 53 54 55 56
+ nupa 59: 61 62 63 64
+ndowna 59: 53 54 55 56
+ nupa 60: 61 62 63 64
+ndowna 60: 53 54 55 56
+ nupa 61:
+ndowna 61: 57 58 59 60
+ nupa 62:
+ndowna 62: 57 58 59 60
+ nupa 63:
+ndowna 63: 57 58 59 60
+ nupa 64:
+ndowna 64: 57 58 59 60
+ REMD Temperature: 250.00000
+====================MD calculation start====================
+ Initial velocities randomly generated
+ Initial velocities
+ 0 0.12886 0.05495 0.00594 0.00000 0.00000 0.00000
+ 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
+ 2 -0.15678 -0.01140 -0.13996 -0.01907 -0.05287 -0.09020
+ 3 0.13945 0.00982 0.14258 -0.00794 -0.01506 0.13649
+ 4 0.08867 0.20048 -0.00070 -0.12014 0.00095 -0.12042
+ 5 -0.26468 -0.26163 -0.04016 -0.18982 -0.08866 0.05577
+ 6 0.02379 -0.08578 0.00111 0.01956 0.02164 0.06186
+ 7 0.12819 0.09785 0.10098 0.02754 0.11147 0.13591
+ 8 -0.14509 0.04829 -0.04514 -0.08097 -0.05546 0.05046
+ 9 0.00076 -0.06136 -0.11724 0.10533 -0.04728 -0.13041
+ 10 0.26677 -0.07152 0.11926 0.06679 0.00076 0.10353
+ 11 -0.37573 0.13788 -0.01625 0.00000 0.00000 0.00000
+ 12 0.25693 -0.01210 0.07525 0.00000 0.00000 0.00000
+ 13 -0.30693 0.08532 -0.09866 -0.02731 0.02783 -0.12092
+ 14 0.37412 0.00837 -0.02785 0.22008 -0.17506 -0.02567
+ 15 -0.12997 -0.03897 0.10342 -0.05840 -0.13283 -0.09576
+ 16 -0.10187 -0.01487 0.01414 0.00000 0.00000 0.00000
+ 17 0.07953 -0.04324 0.04216 0.02274 -0.12698 -0.03734
+ 18 -0.15697 -0.13183 -0.12179 0.12163 -0.01552 -0.05818
+ 19 0.12232 0.08896 -0.00534 0.01069 0.09294 -0.02183
+ 20 -0.07573 -0.15222 0.15039 0.06752 -0.08884 -0.20281
+ 21 0.00000 0.00000 0.00000 0.05227 0.09999 -0.05798
+ 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
+ Calling the zero-angular momentum subroutine
+ vcm right after adjustment:
+ -1.398625787343875E-017 -2.031580523222126E-017 -5.717010517610002E-018
+
+
+ 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) 3.80000 0.00000 0.00000 3.64779 0.96674 1.37044
+LEU( 3) 3.80000 -3.80000 0.00000 2.68687 -3.62474 -1.57795
+TYR( 4) 7.60000 -3.80000 0.00000 7.37548 -2.37399 2.02147
+ILE( 5) 7.60000 -7.60000 0.00000 6.58044 -7.43947 -1.44530
+GLN( 6) 11.40000 -7.60000 0.00000 11.19753 -6.31407 1.82291
+TRP( 7) 11.40000 -11.40000 0.00000 9.90453 -11.16454 -2.11994
+LEU( 8) 15.20000 -11.40000 0.00000 15.02474 -10.28687 1.57795
+LYS( 9) 15.20000 -15.20000 0.00000 13.74127 -14.97033 -2.06786
+ASP( 10) 19.00000 -15.20000 0.00000 18.84553 -14.21890 1.39078
+GLY( 11) 19.00000 -19.00000 0.00000 19.00000 -19.00000 0.00000
+GLY( 12) 22.80000 -19.00000 0.00000 22.80000 -19.00000 0.00000
+PRO( 13) 22.80000 -22.80000 0.00000 22.02787 -22.67843 -1.09456
+SER( 14) 26.60000 -22.80000 0.00000 26.49606 -22.13981 0.93587
+SER( 15) 26.60000 -26.60000 0.00000 25.93981 -26.49606 -0.93587
+GLY( 16) 30.40000 -26.60000 0.00000 30.40000 -26.60000 0.00000
+ARG( 17) 30.40000 -30.40000 0.00000 28.66629 -30.12703 -2.45767
+PRO( 18) 34.20000 -30.40000 0.00000 34.07843 -29.62787 1.09456
+PRO( 19) 34.20000 -34.20000 0.00000 33.42787 -34.07843 -1.09456
+PRO( 20) 38.00000 -34.20000 0.00000 37.87843 -33.42787 1.09456
+SER( 21) 38.00000 -38.00000 0.00000 37.33981 -37.89606 -0.93587
+D ( 22) 41.80000 -38.00000 0.00000 41.80000 -38.00000 0.00000
+
+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 3.800 0.000 0.000 1.684 110.000 -120.000
+LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
+TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
+ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
+GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
+TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
+LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
+LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
+ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
+GLY 11 3.800 90.000 180.000 0.000 180.000 180.000
+GLY 12 3.800 90.000 180.000 0.000 180.000 180.000
+PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
+SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
+SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
+GLY 16 3.800 90.000 180.000 0.000 180.000 180.000
+ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
+PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
+PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
+PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
+SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
+D 22 3.800 90.000 180.000 0.000 180.000 180.000
+ Potential energy and its components
+
+Virtual-chain energies:
+
+EVDW= -1.947821E+01 WEIGHT= 1.352790D+00 (SC-SC)
+EVDW2= 2.387106E+01 WEIGHT= 1.593040D+00 (SC-p)
+EES= -7.520330E+00 WEIGHT= 8.010569D-01 (p-p)
+EVDWPP= -2.624923E+01 WEIGHT= 1.137100D-01 (p-p VDW)
+ESTR= 8.665144E-27 WEIGHT= 1.000000D+00 (stretching)
+EBE= 1.082023E+00 WEIGHT= 1.138730D+00 (bending)
+ESC= 9.168846E+01 WEIGHT= 1.625800D-01 (SC local)
+ETORS= 2.664535E-15 WEIGHT= 2.223965D+00 (torsional)
+ETORSD= -2.547586E+00 WEIGHT= 1.930120D+00 (double torsional)
+EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4= -4.501075E+00 WEIGHT= 5.672548D-01 (multi-body)
+ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
+ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
+EELLO= 2.197932E+01 WEIGHT= 1.970561D-01 (electrostatic-local)
+ETURN3= -1.258124E+00 WEIGHT= 2.073316D+00 (turns, 3rd order)
+ETURN4= 9.498513E+00 WEIGHT= 8.760064D-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= 2.138049E+01 (total)
+
+Initial:
+ Kinetic energy 2.17187E+01
+ potential energy 2.13805E+01
+ total energy 4.30992E+01
+
+ maximum acceleration 9.38160E-01
+
+ Setup time 0.570312500000000
+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 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ MIN ii_write= 1
+ REMD gather times= 48.9648437500000 0.000000000000000E+000
+ REMD writing rst time= 3.906250000000000E-003
+ REMD writing traj time= 3.906250000000000E-003
+ REMD exchange temp,ene
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+ 0.00000 0.00000 0.00000 0.00000 0.00000
+ Enter exchnge, remd_m 4 nodes 64
+ remd_m(1) 4
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+ NREP 16
+ACC 1 250.00000 0.75000 4
+ACC 2 260.00000 1.00000 4
+ACC 3 270.00000 1.00000 4
+ACC 4 280.00000 0.75000 4
+ACC 5 290.00000 0.75000 4
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+ACC 8 320.00000 1.00000 4
+ACC 9 330.00000 0.50000 4
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+ACC 11 350.00000 0.75000 4
+ACC 12 360.00000 0.75000 4
+ACC 13 370.00000 1.00000 4
+ACC 14 380.00000 0.75000 4
+ACC 15 390.00000 0.50000 4
+ 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 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ MIN ii_write= 1
+ REMD gather times= 98.2773437500000 0.000000000000000E+000
+ REMD writing rst time= 3.906250000000000E-003
+ REMD writing traj time= 3.906250000000000E-003
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+ NREP 16
+ACC 1 250.00000 0.75000 8
+ACC 2 260.00000 1.00000 8
+ACC 3 270.00000 0.75000 8
+ACC 4 280.00000 0.62500 8
+ACC 5 290.00000 0.62500 8
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+ REMD scatter time= 0.000000000000000E+000
+ REMD exchange time= 7.812500000000000E-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
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+ MIN ii_write= 1
+ REMD gather times= 147.941406250000 0.000000000000000E+000
+ REMD writing rst time= 3.906250000000000E-003
+ REMD writing traj time= 3.906250000000000E-003
+ REMD exchange temp,ene
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+ NREP 16
+ACC 1 250.00000 0.56250 16
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+ REMD scatter time= 0.000000000000000E+000
+ REMD exchange time= 1.171875000000000E-002
+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
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+ MIN ii_write= 1
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+ REMD writing rst time= 3.906250000000000E-003
+ REMD writing traj time= 3.906250000000000E-003
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+ 0.00000 0.00000 0.00000 0.00000 0.00000
+ Enter exchnge, remd_m 4 nodes 64
+ remd_m(1) 4
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+ NREP 16
+ACC 1 250.00000 0.50000 24
+ACC 2 260.00000 0.75000 24
+ACC 3 270.00000 0.45833 24
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+ACC 5 290.00000 0.50000 24
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+ACC 13 370.00000 0.91667 24
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+ACC 15 390.00000 0.75000 24
+ REMD scatter time= 0.000000000000000E+000
+ REMD exchange time= 1.171875000000000E-002
+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
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+ MIN ii_write= 1
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+ REMD writing rst time= 3.906250000000000E-003
+ REMD writing traj time= 3.906250000000000E-003
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+ NREP 16
+ACC 1 250.00000 0.46429 28
+ACC 2 260.00000 0.67857 28
+ACC 3 270.00000 0.39286 28
+ACC 4 280.00000 0.57143 28
+ACC 5 290.00000 0.50000 28
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+ACC 15 390.00000 0.78571 28
+ REMD scatter time= 0.000000000000000E+000
+ REMD exchange time= 1.171875000000000E-002
+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 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ MIN ii_write= 1
+ REMD gather times= 395.421875000000 0.000000000000000E+000
+ REMD writing rst time= 3.906250000000000E-003
+ REMD writing traj time= 0.000000000000000E+000
+ REMD exchange temp,ene
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+ 0.00000 0.00000 0.00000 0.00000 0.00000
+ Enter exchnge, remd_m 4 nodes 64
+ remd_m(1) 4
+ i 12
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+ i 12
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+ i 7
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+ NREP 16
+ACC 1 250.00000 0.41667 36
+ACC 2 260.00000 0.63889 36
+ACC 3 270.00000 0.41667 36
+ACC 4 280.00000 0.63889 36
+ACC 5 290.00000 0.44444 36
+ACC 6 300.00000 0.61111 36
+ACC 7 310.00000 0.52778 36
+ACC 8 320.00000 0.52778 36
+ACC 9 330.00000 0.72222 36
+ACC 10 340.00000 0.63889 36
+ACC 11 350.00000 0.83333 36
+ACC 12 360.00000 0.77778 36
+ACC 13 370.00000 0.88889 36
+ACC 14 380.00000 0.80556 36
+ACC 15 390.00000 0.80556 36
+ REMD scatter time= 0.000000000000000E+000
+ REMD exchange time= 1.171875000000000E-002
+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 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 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: 1.17188E-02
+ Energy & gradient evaluation: 4.61539E+02
+ Stochastic MD setup: 0.00000E+00
+ Stochastic MD step setup: 0.00000E+00
+ MD steps: 4.94711E+02
+
+
+============================ End of MD calculation ===========================
+CG processor 0 is finishing work.
+ Total wall clock time 495.281250000000 sec
projects / unres.git / blobdiff