+++ /dev/null
---------------------------------------------------------------------------------
- FILE ASSIGNMENT
---------------------------------------------------------------------------------
- Input file : ala10a.inp
- Output file : ala10a.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
- Bond & inertia constant file : ../../PARAM/bond.parm
- Bending parameter file : ../../PARAM/thetaml.5parm
- Rotamer parameter file : ../../PARAM/scgauss.parm
- Threading database : ../../PARAM/patterns.cart
---------------------------------------------------------------------------------
-********************************************************************************
-United-residue force field calculation - serial job.
-********************************************************************************
- ### LAST MODIFIED 6/23/05 7:29PM by czarek
- ++++ Compile info ++++
- Version 2.3 build 2530
- compiled Fri Apr 20 12:08:24 2007
- compiled by adam@matrix
- OS name: Linux
- OS release: 2.4.20-28.7smp
- OS version: #1 SMP Thu Dec 18 11:18:31 EST 2003
- flags:
- FC= mpif90
- OPT = -fast -pc 64 -tp p6 \
- -Minline=name:scalar2,scalar,transpose2,matvec2...
- OPT1 = -C -g -fast -pc 64 -tp p6
- FFLAGS = -c ${OPT}
- FFLAGS1 = -c ${OPT1}
- BIN = ../bin/unres_MD_Tc-pgf90.exe
- LIBS = -L../xdrf -lxdrf
- CPPFLAGS = -DLINUX -DUNRES -DMP -DMPI -DSPLITEL...
- ARCH = LINUX
- PP = /lib/cpp -P
- objectCSA = unres_CSA.o arcos.o cartprint.o cha...
- ++++ 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
-Random seed: -1111333. -1111333
- ran_num 0.3835691052412471
-RMSDBC = 3.0
-RMSDBC1 = 0.5
-RMSDBC1MAX = 1.5
-DRMS = 0.1
-RMSDBCM = 3.0
-Time limit (min): 60.0
- 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: 500000
- Initial time step of numerical integration: 0.10000 natural units
- 4.89000 fs
- Maximum acceleration threshold to scale down the time step: 1.00000
- Maximum predicted energy drift to reduce the timestep: 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)
-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)
-WTURN3= 1.687220 (turns, 3rd order)
-WTURN4= 0.662300 (turns, 4th order)
-WTURN6= 0.000000 (turns, 6th order)
- Reference temperature for weights calculation: 300.0000000000000
- Parameters of the SS-bond potential:
- D0CM 3.780000000000000 AKCM 15.10000000000000 AKTH
- 11.00000000000000 AKCT 12.00000000000000
- V1SS -1.080000000000000 V2SS 7.610000000000000 V3SS
- 13.70000000000000
- EBR -5.500000000000000
- 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 Phi Dsc Alpha Omega
-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
-MD calculation.
-
-********************************************************************************
-
- MODECALC 12
- Calling hpb_partition
- Calling chainbuild
- Calling MD
-====================MD calculation start====================
- Initial velocities randomly generated
- Initial backbone velocities
- -0.1292044072347365 -0.1370883142294474 0.1450622066304738
- 0.1135659089946242 0.2531530570231780 -2.6565029694473186E-002
- -0.1061937693833983 -0.1116623297125810 -0.1582134623125046
- 0.1545984092292579 -9.5458384361267345E-002 0.2197564080243345
- 3.9253268850590239E-002 0.1123725925807762 -0.1841480892990661
- -6.8605618925982661E-002 9.0232818611994965E-002 4.2690022882654546E-002
- 4.2068927420239426E-002 -0.1660727793995226 6.3236006328115888E-002
- -0.2246162891147453 -7.5204025657064495E-002 -4.4972087793837261E-003
- 0.1407143959355549 -3.4615621251325446E-003 0.2201998145518047
- Initial side-chain velocities
- 4.0314066347349105E-002 -7.9452612396078042E-003 -8.4887510982620675E-002
- 0.2391429996690809 6.5174837396261882E-002 -0.2025565503235577
- -5.7929614894672508E-002 -0.1091044722273856 -6.3463220383071519E-002
- 4.3971511738875755E-002 0.1425586201712362 0.1082168256426811
- 2.1022986530089516E-002 -3.7926561161191428E-002 -0.3459376038867435
- -0.3216785073930533 -0.2271802994821818 -2.7866671764172763E-003
- -4.3384536837065637E-002 -5.7857977536535330E-002 -0.1168367005191997
- 5.0313878916894144E-002 8.4990541332738250E-002 -3.4940810102709556E-004
- 0.2124368061520667 -0.1534799359509317 -0.3040129845249302
- 0.3262798718940485 0.2629052218443054 -0.3550178143255543
- Calling the zero-angular momentum subroutine
- vcm right after adjustment:
- -5.3264073145434798E-018 1.5979221943630439E-017 -1.0652814629086960E-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 Phi Dsc Alpha Omega
-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 0.000 180.000
- Potential energy and its components
- 7.475594606447614 -14.66546559980681 10.45502236762420
- -3.731027523592732 -2.225630652057018 0.0000000000000000
- 0.0000000000000000 16.44792980844787 -1.490244503790861
- 6.106255838619212 0.0000000000000000 -2.106037555706406
- 94.24774722083271 0.0000000000000000 -0.9403905000000000
- 0.0000000000000000 -11.71261261559355 1.5345809796877492E-027
- 0.0000000000000000 0.0000000000000000 0.0000000000000000
- 0.0000000000000000
- Initial: Kinetic energy 14.85089585356783 potential energy
- 7.475594606447614 total energy 22.32649046001545
- maximum acceleration 0.1248162499572100
-Velocities reset to random values, time 88.88
-Momenta zeroed out, time 88.88
-Velocities reset to random values, time 179.21
-Momenta zeroed out, time 179.21
-Velocities reset to random values, time 279.03
-Momenta zeroed out, time 279.03
-Velocities reset to random values, time 376.96
-Momenta zeroed out, time 376.96
-Velocities reset to random values, time 463.20
-Momenta zeroed out, time 463.20
-Velocities reset to random values, time 549.28
-Momenta zeroed out, time 549.28
-Velocities reset to random values, time 640.60
-Momenta zeroed out, time 640.60
-Velocities reset to random values, time 730.22
-Momenta zeroed out, time 730.22
-Velocities reset to random values, time 822.00
-Momenta zeroed out, time 822.00
-Velocities reset to random values, time 911.15
-Momenta zeroed out, time 911.15
-Velocities reset to random values, time 1000.95
-Momenta zeroed out, time 1000.95
-Velocities reset to random values, time 1079.98
-Momenta zeroed out, time 1079.98
-Velocities reset to random values, time 1167.48
-Momenta zeroed out, time 1167.48
-Velocities reset to random values, time 1257.26
-Momenta zeroed out, time 1257.26
-Velocities reset to random values, time 1354.14
-Momenta zeroed out, time 1354.14
-Velocities reset to random values, time 1444.25
-Momenta zeroed out, time 1444.25
-Velocities reset to random values, time 1530.30
-Momenta zeroed out, time 1530.30
-Velocities reset to random values, time 1627.09
-Momenta zeroed out, time 1627.09
-Velocities reset to random values, time 1705.22
-Momenta zeroed out, time 1705.22
-Velocities reset to random values, time 1802.16
-Momenta zeroed out, time 1802.16
-Velocities reset to random values, time 1899.95
-Momenta zeroed out, time 1899.95
-Velocities reset to random values, time 1996.36
-Momenta zeroed out, time 1996.36
-Velocities reset to random values, time 2090.43
-Momenta zeroed out, time 2090.43
-Velocities reset to random values, time 2187.85
-Momenta zeroed out, time 2187.85
-Velocities reset to random values, time 2274.17
-Momenta zeroed out, time 2274.17
-Velocities reset to random values, time 2368.28
-Momenta zeroed out, time 2368.28
-Velocities reset to random values, time 2461.69
-Momenta zeroed out, time 2461.69
-Velocities reset to random values, time 2560.64
-Momenta zeroed out, time 2560.64
-Velocities reset to random values, time 2641.79
-Momenta zeroed out, time 2641.79
-Velocities reset to random values, time 2726.00
-Momenta zeroed out, time 2726.00
-Velocities reset to random values, time 2806.89
-Momenta zeroed out, time 2806.89
-Velocities reset to random values, time 2877.56
-Momenta zeroed out, time 2877.56
-Velocities reset to random values, time 2966.17
-Momenta zeroed out, time 2966.17
-Velocities reset to random values, time 3049.35
-Momenta zeroed out, time 3049.35
-Velocities reset to random values, time 3137.69
-Momenta zeroed out, time 3137.69
-Velocities reset to random values, time 3226.05
-Momenta zeroed out, time 3226.05
-Velocities reset to random values, time 3314.36
-Momenta zeroed out, time 3314.36
-Velocities reset to random values, time 3411.10
-Momenta zeroed out, time 3411.10
-Velocities reset to random values, time 3505.08
-Momenta zeroed out, time 3505.08
-Velocities reset to random values, time 3596.55
-Momenta zeroed out, time 3596.55
-Velocities reset to random values, time 3686.71
-Momenta zeroed out, time 3686.71
-Velocities reset to random values, time 3784.64
-Momenta zeroed out, time 3784.64
-Velocities reset to random values, time 3882.12
-Momenta zeroed out, time 3882.12
-Velocities reset to random values, time 3968.46
-Momenta zeroed out, time 3968.46
-Velocities reset to random values, time 4052.70
-Momenta zeroed out, time 4052.70
-Velocities reset to random values, time 4141.42
-Momenta zeroed out, time 4141.42
-Velocities reset to random values, time 4241.01
-Momenta zeroed out, time 4241.01
-Velocities reset to random values, time 4338.25
-Momenta zeroed out, time 4338.25
-Velocities reset to random values, time 4431.99
-Momenta zeroed out, time 4431.99
-Velocities reset to random values, time 4524.93
-Momenta zeroed out, time 4524.93
-Velocities reset to random values, time 4620.72
-Momenta zeroed out, time 4620.72
-Velocities reset to random values, time 4714.34
-Momenta zeroed out, time 4714.34
-Velocities reset to random values, time 4795.98
-Momenta zeroed out, time 4795.98
-Velocities reset to random values, time 4895.98
-Momenta zeroed out, time 4895.98
-Velocities reset to random values, time 4983.23
-Momenta zeroed out, time 4983.23
-Velocities reset to random values, time 5074.97
-Momenta zeroed out, time 5074.97
-Velocities reset to random values, time 5169.77
-Momenta zeroed out, time 5169.77
-Velocities reset to random values, time 5264.99
-Momenta zeroed out, time 5264.99
-Velocities reset to random values, time 5363.19
-Momenta zeroed out, time 5363.19
-Velocities reset to random values, time 5451.27
-Momenta zeroed out, time 5451.27
-Velocities reset to random values, time 5540.56
-Momenta zeroed out, time 5540.56
-Velocities reset to random values, time 5631.51
-Momenta zeroed out, time 5631.51
-Velocities reset to random values, time 5728.79
-Momenta zeroed out, time 5728.79
-Velocities reset to random values, time 5811.69
-Momenta zeroed out, time 5811.69
-Velocities reset to random values, time 5910.36
-Momenta zeroed out, time 5910.36
-Velocities reset to random values, time 6001.17
-Momenta zeroed out, time 6001.17
-Velocities reset to random values, time 6088.08
-Momenta zeroed out, time 6088.08
-Velocities reset to random values, time 6176.08
-Momenta zeroed out, time 6176.08
-Velocities reset to random values, time 6261.77
-Momenta zeroed out, time 6261.77
-Velocities reset to random values, time 6353.33
-Momenta zeroed out, time 6353.33
-Velocities reset to random values, time 6443.11
-Momenta zeroed out, time 6443.11
-Velocities reset to random values, time 6543.11
-Momenta zeroed out, time 6543.11
-Velocities reset to random values, time 6637.02
-Momenta zeroed out, time 6637.02
-Velocities reset to random values, time 6723.82
-Momenta zeroed out, time 6723.82
-Velocities reset to random values, time 6814.68
-Momenta zeroed out, time 6814.68
-Velocities reset to random values, time 6904.03
-Momenta zeroed out, time 6904.03
-Velocities reset to random values, time 6987.21
-Momenta zeroed out, time 6987.21
-Velocities reset to random values, time 7085.01
-Momenta zeroed out, time 7085.01
-Velocities reset to random values, time 7178.21
-Momenta zeroed out, time 7178.21
-Velocities reset to random values, time 7273.75
-Momenta zeroed out, time 7273.75
-Velocities reset to random values, time 7354.90
-Momenta zeroed out, time 7354.90
-Velocities reset to random values, time 7440.93
-Momenta zeroed out, time 7440.93
-Velocities reset to random values, time 7534.36
-Momenta zeroed out, time 7534.36
-Velocities reset to random values, time 7628.33
-Momenta zeroed out, time 7628.33
-Velocities reset to random values, time 7715.46
-Momenta zeroed out, time 7715.46
-Velocities reset to random values, time 7805.58
-Momenta zeroed out, time 7805.58
-Velocities reset to random values, time 7890.30
-Momenta zeroed out, time 7890.30
-Velocities reset to random values, time 7983.28
-Momenta zeroed out, time 7983.28
-Velocities reset to random values, time 8076.52
-Momenta zeroed out, time 8076.52
-Velocities reset to random values, time 8175.05
-Momenta zeroed out, time 8175.05
-Velocities reset to random values, time 8247.40
-Momenta zeroed out, time 8247.40
-Velocities reset to random values, time 8338.93
-Momenta zeroed out, time 8338.93
-Velocities reset to random values, time 8428.66
-Momenta zeroed out, time 8428.66
-Velocities reset to random values, time 8522.79
-Momenta zeroed out, time 8522.79
-Velocities reset to random values, time 8622.79
-Momenta zeroed out, time 8622.79
-Velocities reset to random values, time 8715.90
-Momenta zeroed out, time 8715.90
-Velocities reset to random values, time 8807.60
-Momenta zeroed out, time 8807.60
-Velocities reset to random values, time 8891.80
-Momenta zeroed out, time 8891.80
-Velocities reset to random values, time 8985.42
-Momenta zeroed out, time 8985.42
-Velocities reset to random values, time 9073.97
-Momenta zeroed out, time 9073.97
-Velocities reset to random values, time 9172.41
-Momenta zeroed out, time 9172.41
-Velocities reset to random values, time 9260.67
-Momenta zeroed out, time 9260.67
-Velocities reset to random values, time 9357.66
-Momenta zeroed out, time 9357.66
-Velocities reset to random values, time 9451.31
-Momenta zeroed out, time 9451.31
-Velocities reset to random values, time 9548.27
-Momenta zeroed out, time 9548.27
-Velocities reset to random values, time 9639.63
-Momenta zeroed out, time 9639.63
-Velocities reset to random values, time 9726.37
-Momenta zeroed out, time 9726.37
-Velocities reset to random values, time 9815.50
-Momenta zeroed out, time 9815.50
-Velocities reset to random values, time 9907.32
-Momenta zeroed out, time 9907.32
-Velocities reset to random values, time 9996.48
-Momenta zeroed out, time 9996.48
-Velocities reset to random values, time 10090.64
-Momenta zeroed out, time 10090.64
-Velocities reset to random values, time 10178.13
-Momenta zeroed out, time 10178.13
-Velocities reset to random values, time 10264.86
-Momenta zeroed out, time 10264.86
-Velocities reset to random values, time 10348.06
-Momenta zeroed out, time 10348.06
-Velocities reset to random values, time 10440.58
-Momenta zeroed out, time 10440.58
-Velocities reset to random values, time 10530.44
-Momenta zeroed out, time 10530.44
-Velocities reset to random values, time 10628.06
-Momenta zeroed out, time 10628.06
-Velocities reset to random values, time 10716.02
-Momenta zeroed out, time 10716.02
-Velocities reset to random values, time 10812.13
-Momenta zeroed out, time 10812.13
-Velocities reset to random values, time 10893.64
-Momenta zeroed out, time 10893.64
-Velocities reset to random values, time 10987.43
-Momenta zeroed out, time 10987.43
-Velocities reset to random values, time 11082.47
-Momenta zeroed out, time 11082.47
-Velocities reset to random values, time 11177.41
-Momenta zeroed out, time 11177.41
-Velocities reset to random values, time 11261.41
-Momenta zeroed out, time 11261.41
-Velocities reset to random values, time 11349.95
-Momenta zeroed out, time 11349.95
-Velocities reset to random values, time 11448.83
-Momenta zeroed out, time 11448.83
-Velocities reset to random values, time 11532.90
-Momenta zeroed out, time 11532.90
-Velocities reset to random values, time 11625.22
-Momenta zeroed out, time 11625.22
-Velocities reset to random values, time 11717.97
-Momenta zeroed out, time 11717.97
-Velocities reset to random values, time 11795.42
-Momenta zeroed out, time 11795.42
-Velocities reset to random values, time 11890.82
-Momenta zeroed out, time 11890.82
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\ No newline at end of file
projects / unres.git / blobdiff