X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=examples%2Funres%2Fnew%2FMD%2FDYN_SS%2Fdyn_ss%2Fcheckgrad%2Fsmall.out_GB000;fp=examples%2Funres%2Fnew%2FMD%2FDYN_SS%2Fdyn_ss%2Fcheckgrad%2Fsmall.out_GB000;h=cd100a0d6820d6b48401b8c3526cb7f63a1bb002;hb=d71184aad2eded5a73627e8bc9296597319c9e59;hp=0000000000000000000000000000000000000000;hpb=b09212e2812655f95553a0f781fe148994a2091c;p=unres.git diff --git a/examples/unres/new/MD/DYN_SS/dyn_ss/checkgrad/small.out_GB000 b/examples/unres/new/MD/DYN_SS/dyn_ss/checkgrad/small.out_GB000 new file mode 100644 index 0000000..cd100a0 --- /dev/null +++ b/examples/unres/new/MD/DYN_SS/dyn_ss/checkgrad/small.out_GB000 @@ -0,0 +1,657 @@ +-------------------------------------------------------------------------------- + FILE ASSIGNMENT +-------------------------------------------------------------------------------- + Input file : small.inp + Output file : small.out_GB000 + + 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 +-------------------------------------------------------------------------------- +******************************************************************************** +United-residue force field calculation - parallel job. +******************************************************************************** + ### LAST MODIFIED 03/28/12 23:29 by czarek + ++++ Compile info ++++ + Version 3.1 build 43 + compiled Fri Feb 15 05:04:12 2013 + 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: + 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 ... + LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr... + 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_MP... + 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 + MPI: node= 0 iseed(4)= 0 0 -16 + -62756 + ran_num 6.422640197456531E-013 +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. + +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= 0.145810 (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 correlatkion) +WTURN3= 2.913860 (turns, 3rd order) +WTURN4= 0.731780 (turns, 4th order) +WTURN6= 0.023910 (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 3.59866156847500 + 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= 0 ihpb,jhpb: +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 + Running with dynamic disulfide-bond formation + Processor 0 CG group 0 absolute rank 0 nhpb + 0 link_start= 1 link_end 0 + + +******************************************************************************** + Processor 0: end reading molecular data. +******************************************************************************** + + +Checking energy gradient calculation. + +******************************************************************************** + + nset 0 nfrag 0 npair 0 nfrag_back 0 + + + 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 + dyn_ssbond_ene -1.212205582757399E-004 + +Virtual-chain energies: + +EVDW= -1.784028E+01 WEIGHT= 1.000000E+00 (SC-SC) +EVDW2= 2.118779E+01 WEIGHT= 2.794050E+00 (SC-p) +EES= -8.122745E+00 WEIGHT= 1.458100E-01 (p-p) +EVDWPP= -2.540621E+01 WEIGHT= 1.458100E-01 (p-p VDW) +ESTR= 4.237046E-27 WEIGHT= 1.000000E+00 (stretching) +EBE= -1.185178E+00 WEIGHT= 1.956840E+00 (bending) +ESC= 1.520408E+02 WEIGHT= 1.701000E-01 (SC local) +ETORS= 0.000000E+00 WEIGHT= 2.046980E+00 (torsional) +ETORSD= -2.194244E+00 WEIGHT= 1.696240E+00 (double torsional) +EHPB= 0.000000E+00 WEIGHT= 1.000000E+00 (SS bridges & dist. cnstr.) +ECORR4= -5.324225E+00 WEIGHT= 1.846150E+00 (multi-body) +ECORR5= 2.317900E+01 WEIGHT= 2.730000E-02 (multi-body) +ECORR6= 1.215220E+01 WEIGHT= 7.410000E-03 (multi-body) +EELLO= 3.759544E+01 WEIGHT= 1.218370E+00 (electrostatic-local) +ETURN3= -3.193381E+00 WEIGHT= 2.913860E+00 (turns, 3rd order) +ETURN4= 1.424793E+01 WEIGHT= 7.317800E-01 (turns, 4th order) +ETURN6= 0.000000E+00 WEIGHT= 2.391000E-02 (turns, 6th order) +ESCCOR= 7.779132E+00 WEIGHT= 1.000000E+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= 1.018907E+02 (total) + Uconst 0.000000000000000E+000 Uconst_back 0.000000000000000E+000 + +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 + Calling CHECK_ECARTINT. + dyn_ssbond_ene -1.212205582757399E-004 + +Virtual-chain energies: + +EVDW= -1.784028E+01 WEIGHT= 1.000000E+00 (SC-SC) +EVDW2= 2.118779E+01 WEIGHT= 2.794050E+00 (SC-p) +EES= -8.122745E+00 WEIGHT= 1.458100E-01 (p-p) +EVDWPP= -2.540621E+01 WEIGHT= 1.458100E-01 (p-p VDW) +ESTR= 4.237046E-27 WEIGHT= 1.000000E+00 (stretching) +EBE= -1.185178E+00 WEIGHT= 1.956840E+00 (bending) +ESC= 1.520408E+02 WEIGHT= 1.701000E-01 (SC local) +ETORS= 0.000000E+00 WEIGHT= 2.046980E+00 (torsional) +ETORSD= -2.194244E+00 WEIGHT= 1.696240E+00 (double torsional) +EHPB= 0.000000E+00 WEIGHT= 1.000000E+00 (SS bridges & dist. cnstr.) +ECORR4= -5.324225E+00 WEIGHT= 1.846150E+00 (multi-body) +ECORR5= 2.317900E+01 WEIGHT= 2.730000E-02 (multi-body) +ECORR6= 1.215220E+01 WEIGHT= 7.410000E-03 (multi-body) +EELLO= 3.759544E+01 WEIGHT= 1.218370E+00 (electrostatic-local) +ETURN3= -3.193381E+00 WEIGHT= 2.913860E+00 (turns, 3rd order) +ETURN4= 1.424793E+01 WEIGHT= 7.317800E-01 (turns, 4th order) +ETURN6= 0.000000E+00 WEIGHT= 2.391000E-02 (turns, 6th order) +ESCCOR= 7.779132E+00 WEIGHT= 1.000000E+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= 1.018907E+02 (total) + enter cartgrad + exit cartgrad + 1 0.00000 0.00000 0.00000 + 2 0.00000 0.00000 0.00000 + 3 0.00000 0.00000 0.00000 + 4 0.00000 0.00000 0.00000 + 5 0.00000 0.00000 0.00000 + 6 0.00000 0.00000 0.00000 + 7 0.00000 0.00000 0.00000 + 8 0.00000 0.00000 0.00000 + 9 0.00000 0.00000 0.00000 + 10 0.00000 0.00000 0.00000 + 11 0.00000 0.00000 0.00000 + 12 0.00000 0.00000 0.00000 + 13 0.00000 0.00000 0.00000 + 14 0.00000 0.00000 0.00000 + 15 0.00000 0.00000 0.00000 + 16 0.00000 0.00000 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