--- /dev/null
+--------------------------------------------------------------------------------
+ FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file : ala10-cx.inp
+ Output file : ala10-cx.out_GB
+
+ Sidechain potential file :
+ ../../../../PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
+ SCp potential file : ../../../../PARAM/scp.parm
+ Electrostatic potential file : ../../../../PARAM/electr_631Gdp.parm
+ Cumulant coefficient file :
+ ../../../../PARAM/fourier_opt.parm.1igd_hc_iter3_3
+ Torsional parameter file : ../../../../PARAM/torsion_631Gdp.parm
+ Double torsional parameter file : ../../../../PARAM/torsion_double_631Gdp.parm
+ SCCOR parameter file : ../../../../PARAM/rotcorr_AM1.parm
+ Bond & inertia constant file : ../../../../PARAM/bond.parm
+ Bending parameter file : ../../../../PARAM/thetaml.5parm
+ Rotamer parameter file : ../../../../PARAM/scgauss.parm
+ Threading database : ../../../../PARAM/patterns.cart
+--------------------------------------------------------------------------------
+ ### LAST MODIFIED 03/28/12 23:29 by czarek
+ ++++ Compile info ++++
+ Version 2.5 build 34
+ compiled Mon Apr 2 08:16:44 2012
+ compiled by adam@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:
+ 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: 10000
+ Initial time step of numerical integration: 0.10000 natural units
+ 4.89000 fs
+Maximum acceleration threshold to reduce the time step/increase split number: 1.00000
+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: 1000
+Berendsen bath calculation
+ Temperature: 300.00000
+ Coupling constant (tau): 0.10000
+Momenta will be reset at zero every 1000 steps
+Velocities will be reset at random every 1000 steps
+
+============================== 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= 1.000000 (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= 1.000000 (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
+ ITEL
+ 1 21 0
+ 2 9 1
+ 3 9 1
+ 4 9 1
+ 5 9 1
+ 6 9 1
+ 7 9 1
+ 8 9 1
+ 9 9 1
+ 10 9 1
+ 11 9 0
+ ns= 0 iss:
+Boundaries in phi angle sampling:
+D 1 -180.0 180.0
+ALA 2 -180.0 180.0
+ALA 3 -180.0 180.0
+ALA 4 -180.0 180.0
+ALA 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
+D 12 -180.0 180.0
+ NZ_START= 2 NZ_END= 11
+ IZ_SC= 0
+Initial geometry will be read in.
+
+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
+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
+ALA 5 3.800 90.000 180.000 0.743 100.000 -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
+D 12 3.800 90.000 180.000 0.000 0.000 0.000
+Mesoscopic molecular dynamics (MD) calculation.
+
+********************************************************************************
+
+ Calling chainbuild
+====================MD calculation start====================
+ Initial velocities randomly generated
+ Initial velocities
+ 0 -0.02571 0.04778 -0.01151 0.00000 0.00000 0.00000
+ 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
+ 2 -0.11082 -0.24316 -0.01092 -0.01544 0.04693 0.02901
+ 3 0.17509 0.14021 0.01920 -0.06074 0.20983 -0.00546
+ 4 -0.28110 -0.18298 0.04141 0.05768 -0.02663 -0.10403
+ 5 0.52321 0.32791 -0.28506 0.24480 0.23049 0.08887
+ 6 -0.24047 -0.12903 0.12193 0.03851 -0.08315 0.33390
+ 7 0.09902 -0.00280 0.29189 -0.33532 -0.00436 0.03329
+ 8 -0.12228 0.11945 -0.17716 0.08467 -0.09409 -0.31636
+ 9 0.15147 -0.14801 -0.02818 0.01545 -0.19775 0.03783
+ 10 0.03113 0.28957 -0.29450 0.09912 -0.08052 0.16164
+ 11 0.00000 0.00000 0.00000 -0.24131 -0.01384 0.16566
+ 12 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
+ Calling the zero-angular momentum subroutine
+ vcm right after adjustment:
+ -2.929524022998914E-017 -5.326407314543479E-018 -1.731082377226631E-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
+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
+ALA( 5) 7.60000 -7.60000 0.00000 7.25007 -7.43253 -0.63368
+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
+D ( 12) 22.80000 -19.00000 0.00000 22.80000 -19.00000 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
+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
+ALA 5 3.800 90.000 180.000 0.743 100.000 -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
+D 12 3.800 90.000 180.000 0.000 180.000 180.000
+ Potential energy and its components
+
+Virtual-chain energies:
+
+EVDW= -1.466547E+01 WEIGHT= 1.352790D+00 (SC-SC)
+EVDW2= 1.045502E+01 WEIGHT= 1.593040D+00 (SC-p)
+EES= -3.731028E+00 WEIGHT= 7.153400D-01 (p-p)
+EVDWPP= -1.171261E+01 WEIGHT= 1.137100D-01 (p-p VDW)
+ESTR= 1.531499E-27 WEIGHT= 1.000000D+00 (stretching)
+EBE= -2.106038E+00 WEIGHT= 1.138730D+00 (bending)
+ESC= 9.424775E+01 WEIGHT= 1.625800D-01 (SC local)
+ETORS= 0.000000E+00 WEIGHT= 1.985990D+00 (torsional)
+ETORSD= -9.403905E-01 WEIGHT= 1.570690D+00 (double torsional)
+EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4= -2.225631E+00 WEIGHT= 4.288700D-01 (multi-body)
+ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
+ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
+EELLO= 1.644793E+01 WEIGHT= 1.603600D-01 (electrostatic-local)
+ETURN3= -1.490245E+00 WEIGHT= 1.687220D+00 (turns, 3rd order)
+ETURN4= 6.106256E+00 WEIGHT= 6.623000D-01 (turns, 4th order)
+ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
+ESCCOR= 0.000000E+00 WEIGHT= 1.000000D+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= 7.475595E+00 (total)
+
+Initial:
+ Kinetic energy 1.64667E+01
+ potential energy 7.47559E+00
+ total energy 2.39423E+01
+
+ maximum acceleration 9.73465E-01
+
+Velocities reset to random values, time 84.93
+Momenta zeroed out, time 84.93
+Velocities reset to random values, time 162.90
+Momenta zeroed out, time 162.90
+Velocities reset to random values, time 249.85
+Momenta zeroed out, time 249.85
+Velocities reset to random values, time 319.31
+Momenta zeroed out, time 319.31
+Velocities reset to random values, time 398.92
+Momenta zeroed out, time 398.92
+Velocities reset to random values, time 476.10
+Momenta zeroed out, time 476.10
+Velocities reset to random values, time 540.82
+Momenta zeroed out, time 540.82
+Velocities reset to random values, time 612.01
+Momenta zeroed out, time 612.01
+Velocities reset to random values, time 687.88
+Momenta zeroed out, time 687.88
+Velocities reset to random values, time 762.77
+Momenta zeroed out, time 762.77
+
+
+=================================== Timing ===================================
+
+ MD calculations setup: 0.00000E+00
+ Energy & gradient evaluation: 7.80000E-01
+ Stochastic MD setup: 0.00000E+00
+ Stochastic MD step setup: 0.00000E+00
+ MD steps: 8.80000E-01
+
+
+============================ End of MD calculation ===========================
+
+
+***** Computation time: 0 hours 0 minutes 1 seconds *****
projects / unres.git / blobdiff