X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=examples%2Funres%2Fnew%2FMD%2FDYN_SS%2Fss%2Fsmall.out_GB;fp=examples%2Funres%2Fnew%2FMD%2FDYN_SS%2Fss%2Fsmall.out_GB;h=0000000000000000000000000000000000000000;hb=3fc7e5eaa3b384501e4864c64ade3c92121fa283;hp=3fb6650e3fe24e77ccfe196ce503381f8c556d9e;hpb=fbb1880ba2f52309ca4d0545f1799a181ffcbd81;p=unres.git diff --git a/examples/unres/new/MD/DYN_SS/ss/small.out_GB b/examples/unres/new/MD/DYN_SS/ss/small.out_GB deleted file mode 100644 index 3fb6650..0000000 --- a/examples/unres/new/MD/DYN_SS/ss/small.out_GB +++ /dev/null @@ -1,391 +0,0 @@ --------------------------------------------------------------------------------- - FILE ASSIGNMENT --------------------------------------------------------------------------------- - Input file : small.inp - Output file : small.out_GB - - Sidechain potential file : - /users/czarek/UNRES/GIT/unres/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16- - 10-8k - SCp potential file : /users/czarek/UNRES/GIT/unres/PARAM/scp.parm - Electrostatic potential file : - /users/czarek/UNRES/GIT/unres/PARAM/electr_631Gdp.parm - Cumulant coefficient file : - /users/czarek/UNRES/GIT/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3 - Torsional parameter file : - /users/czarek/UNRES/GIT/unres/PARAM/torsion_631Gdp.parm - Double torsional parameter file : - /users/czarek/UNRES/GIT/unres/PARAM/torsion_double_631Gdp.parm - SCCOR parameter file : /users/czarek/UNRES/GIT/unres/PARAM/sccor_pdb_shelly.dat - Bond & inertia constant file : /users/czarek/UNRES/GIT/unres/PARAM/bond.parm - Bending parameter file : - /users/czarek/UNRES/GIT/unres/PARAM/thetaml.5parm - Rotamer parameter file : - /users/czarek/UNRES/GIT/unres/PARAM/scgauss.parm - Threading database : - /users/czarek/UNRES/GIT/unres/PARAM/patterns.cart --------------------------------------------------------------------------------- - ### LAST MODIFIED 03/28/12 23:29 by czarek - ++++ Compile info ++++ - Version 3.1 build 27 - compiled Fri Oct 5 13:10:24 2012 - compiled by czarek@piasek3 - OS name: Linux - OS release: 2.6.32-42-generic - OS version: #96-Ubuntu SMP Wed Aug 15 19:37:37 UTC 2012 - 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: 50000 - Initial time step of numerical integration: 0.10000 natural units - 4.89000 fs -Maximum acceleration threshold to reduce the time step/increase split number: 5.00000 -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: 1000 - Frequency of coordinate output: 300 -Berendsen bath calculation - Temperature: 400.00000 - Coupling constant (tau): 1.00000 -Momenta will be reset at zero every 1000 steps - -============================== End of MD run setup ============================= - - -Energy-term weights (unscaled): - -WSCC= 1.000000 (SC-SC) -WSCP= 2.794050 (SC-p) -WELEC= 0.145810 (p-p electr) -WVDWPP= 0.145810 (p-p VDW) -WBOND= 1.000000 (stretching) -WANG= 1.956840 (bending) -WSCLOC= 0.170100 (SC local) -WTOR= 2.046980 (torsional) -WTORD= 1.696240 (double torsional) -WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) -WEL_LOC= 1.218370 (multi-body 3-rd order) -WCORR4= 1.846150 (multi-body 4th order) -WCORR5= 0.027300 (multi-body 5th order) -WCORR6= 0.007410 (multi-body 6th order) -WSCCOR= 1.000000 (back-scloc correlation) -WTURN3= 2.913860 (turns, 3rd order) -WTURN4= 0.731780 (turns, 4th order) -WTURN6= 0.023910 (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= 2.794050 (SC-p) -WELEC= 0.117327 (p-p electr) -WVDWPP= 0.145810 (p-p VDW) -WBOND= 1.000000 (stretching) -WANG= 1.956840 (bending) -WSCLOC= 0.170100 (SC local) -WTOR= 1.647115 (torsional) -WTORD= 1.058472 (double torsional) -WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) -WEL_LOC= 0.760276 (multi-body 3-rd order) -WCORR4= 0.874494 (multi-body 4th order) -WCORR5= 0.009729 (multi-body 5th order) -WCORR6= 0.001982 (multi-body 6th order) -WSCCOR= 0.804656 (back-scloc correlatkion) -WTURN3= 1.818280 (turns, 3rd order) -WTURN4= 0.346633 (turns, 4th order) -WTURN6= 0.006394 (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 SS_DEPTH -6.90133843152500 - HT 0.000000000000000E+000 - ITEL - 1 10 1 - 2 9 1 - 3 9 1 - 4 9 1 - 5 1 1 - 6 9 1 - 7 9 1 - 8 9 1 - 9 9 1 - 10 9 1 - 11 9 1 - 12 9 1 - 13 9 1 - 14 1 1 - 15 9 1 - 16 9 1 - 17 9 1 - ns= 2 iss: 5 14 - nss= 1 ihpb,jhpb: 5 14 -Boundaries in phi angle sampling: -GLY 1 -180.0 180.0 -ALA 2 -180.0 180.0 -ALA 3 -180.0 180.0 -ALA 4 -180.0 180.0 -CYS 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 -ALA 12 -180.0 180.0 -ALA 13 -180.0 180.0 -CYS 14 -180.0 180.0 -ALA 15 -180.0 180.0 -ALA 16 -180.0 180.0 -ALA 17 -180.0 180.0 -GLY 18 -180.0 180.0 - NZ_START= 1 NZ_END= 18 - IZ_SC= 0 -Initial geometry will be read in. - -Geometry of the virtual chain. - Res d Theta Gamma Dsc Alpha Beta -GLY 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 -CYS 5 3.800 90.000 180.000 1.237 100.000 -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 -ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000 -ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000 -CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000 -ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000 -ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000 -ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000 -GLY 18 3.800 90.000 180.000 0.000 0.000 0.000 - -The chain contains 2 disulfide-bridging cysteines. - 5 14 - -Pre-formed links are: - -CYS( 5) -- CYS( 14) 0.000 -5.500 0.000 - -Mesoscopic molecular dynamics (MD) calculation. - -******************************************************************************** - - Calling chainbuild -====================MD calculation start==================== - Initial velocities randomly generated - Initial velocities - 0 -0.33453 -0.07483 -0.03206 0.00000 0.00000 0.00000 - 1 0.60801 0.09078 -0.01649 0.00000 0.00000 0.00000 - 2 -0.22717 -0.43486 0.29485 0.06489 -0.21337 0.35299 - 3 0.15327 0.53566 -0.23305 -0.24688 -0.00986 -0.12275 - 4 0.06228 -0.05375 0.06294 -0.19345 0.02670 0.20836 - 5 -0.33309 0.05139 -0.01429 -0.12351 -0.00675 -0.09273 - 6 -0.06817 -0.22870 -0.04737 0.20671 -0.13568 -0.21386 - 7 0.50143 0.23749 0.03096 -0.16319 0.01175 -0.03820 - 8 -0.13754 0.04563 0.12172 -0.02843 -0.01504 -0.10702 - 9 -0.11966 -0.06273 0.01098 -0.25787 -0.12974 -0.03183 - 10 -0.29196 -0.21182 -0.28091 -0.13032 -0.00023 -0.02943 - 11 0.17078 0.30325 0.24474 0.21168 -0.19118 0.08836 - 12 -0.02379 -0.04666 -0.03493 0.00932 -0.18572 -0.02650 - 13 0.26454 -0.06093 -0.40002 0.19547 -0.19792 0.00495 - 14 -0.36457 -0.27710 0.61404 -0.15632 0.07442 0.10234 - 15 0.14723 0.29638 -0.15981 0.45708 -0.09130 0.03430 - 16 -0.02356 0.03470 -0.42550 0.09899 -0.15554 -0.09256 - 17 0.09038 -0.11432 0.34794 -0.14072 0.01732 0.14744 - 18 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 - Calling the zero-angular momentum subroutine - vcm right after adjustment: - 1.312320360077017E-019 2.014411752718222E-017 -9.448706592554524E-018 - - - alpha-carbon coordinates centroid coordinates - X Y Z X Y Z -GLY( 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 -CYS( 5) 7.60000 -7.60000 0.00000 7.01741 -7.32119 -1.05500 -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 -ALA( 12) 22.80000 -19.00000 0.00000 22.73284 -18.57346 0.60465 -ALA( 13) 22.80000 -22.80000 0.00000 22.45007 -22.63253 -0.63368 -CYS( 14) 26.60000 -22.80000 0.00000 26.48819 -22.08987 1.00667 -ALA( 15) 26.60000 -26.60000 0.00000 26.25007 -26.43253 -0.63368 -ALA( 16) 30.40000 -26.60000 0.00000 30.33284 -26.17346 0.60465 -ALA( 17) 30.40000 -30.40000 0.00000 29.97346 -30.33284 -0.60465 -GLY( 18) 34.20000 -30.40000 0.00000 34.20000 -30.40000 0.00000 - -Geometry of the virtual chain. - Res d Theta Gamma Dsc Alpha Beta -GLY 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 -CYS 5 3.800 90.000 180.000 1.237 100.000 -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 -ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000 -ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000 -CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000 -ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000 -ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000 -ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000 -GLY 18 3.800 90.000 180.000 0.000 180.000 180.000 - Potential energy and its components - -Virtual-chain energies: - -EVDW= -1.784016E+01 WEIGHT= 1.000000D+00 (SC-SC) -EVDW2= 2.118779E+01 WEIGHT= 2.794050D+00 (SC-p) -EES= -8.122745E+00 WEIGHT= 1.173269D-01 (p-p) -EVDWPP= -2.540621E+01 WEIGHT= 1.458100D-01 (p-p VDW) -ESTR= 4.237046E-27 WEIGHT= 1.000000D+00 (stretching) -EBE= -1.185178E+00 WEIGHT= 1.956840D+00 (bending) -ESC= 1.520408E+02 WEIGHT= 1.701000D-01 (SC local) -ETORS= 0.000000E+00 WEIGHT= 1.647115D+00 (torsional) -ETORSD= -2.194244E+00 WEIGHT= 1.058472D+00 (double torsional) -EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) -ECORR4= 0.000000E+00 WEIGHT= 8.744941D-01 (multi-body) -ECORR5= 2.317900E+01 WEIGHT= 9.728750D-03 (multi-body) -ECORR6= 1.215220E+01 WEIGHT= 1.981519D-03 (multi-body) -EELLO= 3.759544E+01 WEIGHT= 7.602761D-01 (electrostatic-local) -ETURN3= -3.193381E+00 WEIGHT= 1.818280D+00 (turns, 3rd order) -ETURN4= 1.424793E+01 WEIGHT= 3.466334D-01 (turns, 4th order) -ETURN6= 0.000000E+00 WEIGHT= 6.393807D-03 (turns, 6th order) -ESCCOR= 7.779132E+00 WEIGHT= 8.046559D-01 (backbone-rotamer corr) -EDIHC= 0.000000E+00 (dihedral angle constraints) -ESS= -5.500000E+00 (disulfide-bridge intrinsic energy) -UCONST= 0.000000E+00 (Constraint energy) -ETOT= 8.664685E+01 (total) - -Initial: - Kinetic energy 4.43916E+01 - potential energy 8.66468E+01 - total energy 1.31038E+02 - - maximum acceleration 4.30607E+00 - -Momenta zeroed out, time 82.24 -Momenta zeroed out, time 167.24 -Momenta zeroed out, time 256.61 -Momenta zeroed out, time 336.19 -Momenta zeroed out, time 424.42 -Momenta zeroed out, time 501.35 -Momenta zeroed out, time 594.96 -Momenta zeroed out, time 676.75 -Momenta zeroed out, time 763.06 -Momenta zeroed out, time 852.52 -Momenta zeroed out, time 929.93 -Momenta zeroed out, time 1011.97 -Momenta zeroed out, time 1086.41 -Momenta zeroed out, time 1172.78 -Momenta zeroed out, time 1244.29 -Momenta zeroed out, time 1327.03 -Momenta zeroed out, time 1414.35 -Momenta zeroed out, time 1505.75 -Momenta zeroed out, time 1588.07 -Momenta zeroed out, time 1682.50 -Momenta zeroed out, time 1761.66 -Momenta zeroed out, time 1842.58 -Momenta zeroed out, time 1924.54 -Momenta zeroed out, time 2006.16 -Momenta zeroed out, time 2095.77 -Momenta zeroed out, time 2174.07 -Momenta zeroed out, time 2250.48 -Momenta zeroed out, time 2327.93 -Momenta zeroed out, time 2415.08 -Momenta zeroed out, time 2484.46 -Momenta zeroed out, time 2553.97 -Momenta zeroed out, time 2639.64 -Momenta zeroed out, time 2715.89 -Momenta zeroed out, time 2803.24 -Momenta zeroed out, time 2888.74 -Momenta zeroed out, time 2967.55 -Momenta zeroed out, time 3050.82 -Momenta zeroed out, time 3139.25 -Momenta zeroed out, time 3220.06 -Momenta zeroed out, time 3310.99 -Momenta zeroed out, time 3386.65 -Momenta zeroed out, time 3462.21 -Momenta zeroed out, time 3542.12 -Momenta zeroed out, time 3625.49 -Momenta zeroed out, time 3713.61 -Momenta zeroed out, time 3793.08 -Momenta zeroed out, time 3876.16 -Momenta zeroed out, time 3955.62 -Momenta zeroed out, time 4032.18 -Momenta zeroed out, time 4113.16 - - -=================================== Timing =================================== - - MD calculations setup: 1.00000E-02 - Energy & gradient evaluation: 2.00600E+01 - Stochastic MD setup: 0.00000E+00 - Stochastic MD step setup: 0.00000E+00 - MD steps: 2.10900E+01 - - -============================ End of MD calculation =========================== - - -***** Computation time: 0 hours 0 minutes 21 seconds *****