+++ /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