X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=examples%2Funres%2Fnew%2Fmicrocanonical%2FVTS%2Fff_1l2y%2F1L2Y_micro.out_GB000;h=d1c2aeb28bf4f92b96f07fd8a2310f368bcab585;hb=d5f5162b182a8b2f7a40d50b6877beb2a52297bc;hp=1612412f93996e2b3abe1c910a260f37bd34e19c;hpb=0159dffb0c6ab8021f45dc01794d77b091499a4d;p=unres.git diff --git a/examples/unres/new/microcanonical/VTS/ff_1l2y/1L2Y_micro.out_GB000 b/examples/unres/new/microcanonical/VTS/ff_1l2y/1L2Y_micro.out_GB000 index 1612412..d1c2aeb 100644 --- a/examples/unres/new/microcanonical/VTS/ff_1l2y/1L2Y_micro.out_GB000 +++ b/examples/unres/new/microcanonical/VTS/ff_1l2y/1L2Y_micro.out_GB000 @@ -83,9 +83,9 @@ velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2 energy: kcal/mol, temperature: K Number of time steps: 1000000 - Initial time step of numerical integration: 0.10000 natural units - 4.89000 fs -Maximum acceleration threshold to reduce the time step/increase split number: 10.00000 + Initial time step of numerical integration: 0.01000 natural units + 0.48900 fs +Maximum acceleration threshold to reduce the time step/increase split number: 20.00000 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: 10000 @@ -240,32 +240,31 @@ nsup= 20 12 PRO 20 LEU 3 13 PRO 20 TYR 4 14 PRO 20 TRP 7 -Extended chain initial geometry. 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 -ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000 -LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000 -TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000 -ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000 -GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000 -TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000 -LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000 -LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000 -ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000 -GLY 11 3.800 90.000 180.000 0.000 110.000 -120.000 -GLY 12 3.800 90.000 180.000 0.000 110.000 -120.000 -PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000 -SER 14 3.800 90.000 180.000 1.150 110.000 -120.000 -SER 15 3.800 90.000 180.000 1.150 110.000 -120.000 -GLY 16 3.800 90.000 180.000 0.000 110.000 -120.000 -ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000 -PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000 -PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000 -PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000 -SER 21 3.800 90.000 180.000 1.150 110.000 -120.000 -D 22 3.800 90.000 180.000 0.000 0.000 0.000 +ASN 2 3.861 0.000 0.000 1.977 94.624 -178.093 +LEU 3 3.876 92.239 0.000 2.195 102.878 -79.236 +TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440 +ILE 5 3.871 90.357 45.849 1.692 144.011 -104.516 +GLN 6 3.846 89.090 55.194 2.338 170.986 -139.318 +TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913 +LEU 8 3.859 93.032 48.298 2.105 151.723 -105.899 +LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960 +ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646 +GLY 11 3.891 89.908 56.679 0.000 0.000 0.000 +GLY 12 3.864 100.181 -87.304 0.000 0.000 0.000 +PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580 +SER 14 3.876 89.537 4.261 1.267 144.515 -129.218 +SER 15 3.875 91.815 66.108 1.262 161.047 -100.177 +GLY 16 3.866 101.784 70.140 0.000 0.000 0.000 +ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716 +PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024 +PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417 +PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207 +SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341 +D 22 3.858 114.201 180.000 0.000 0.000 0.000 ******************************************************************************** @@ -306,103 +305,103 @@ Mesoscopic molecular dynamics (MD) calculation. 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 Calling the zero-angular momentum subroutine vcm right after adjustment: - 1.837610523517500E-017 -2.960594732333751E-018 9.596410511702503E-018 + 4.226504204090251E-017 -1.020894735287500E-018 -4.083578941150001E-019 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 -ASN( 2) 3.80000 0.00000 0.00000 3.64779 0.96674 1.37044 -LEU( 3) 3.80000 -3.80000 0.00000 2.68687 -3.62474 -1.57795 -TYR( 4) 7.60000 -3.80000 0.00000 7.37548 -2.37399 2.02147 -ILE( 5) 7.60000 -7.60000 0.00000 6.58044 -7.43947 -1.44530 -GLN( 6) 11.40000 -7.60000 0.00000 11.19753 -6.31407 1.82291 -TRP( 7) 11.40000 -11.40000 0.00000 9.90453 -11.16454 -2.11994 -LEU( 8) 15.20000 -11.40000 0.00000 15.02474 -10.28687 1.57795 -LYS( 9) 15.20000 -15.20000 0.00000 13.74127 -14.97033 -2.06786 -ASP( 10) 19.00000 -15.20000 0.00000 18.84553 -14.21890 1.39078 -GLY( 11) 19.00000 -19.00000 0.00000 19.00000 -19.00000 0.00000 -GLY( 12) 22.80000 -19.00000 0.00000 22.80000 -19.00000 0.00000 -PRO( 13) 22.80000 -22.80000 0.00000 22.02787 -22.67843 -1.09456 -SER( 14) 26.60000 -22.80000 0.00000 26.49606 -22.13981 0.93587 -SER( 15) 26.60000 -26.60000 0.00000 25.93981 -26.49606 -0.93587 -GLY( 16) 30.40000 -26.60000 0.00000 30.40000 -26.60000 0.00000 -ARG( 17) 30.40000 -30.40000 0.00000 28.66629 -30.12703 -2.45767 -PRO( 18) 34.20000 -30.40000 0.00000 34.07843 -29.62787 1.09456 -PRO( 19) 34.20000 -34.20000 0.00000 33.42787 -34.07843 -1.09456 -PRO( 20) 38.00000 -34.20000 0.00000 37.87843 -33.42787 1.09456 -SER( 21) 38.00000 -38.00000 0.00000 37.33981 -37.89606 -0.93587 -D ( 22) 41.80000 -38.00000 0.00000 41.80000 -38.00000 0.00000 +ASN( 2) 3.86050 0.00000 0.00000 2.55159 1.47985 0.06557 +LEU( 3) 4.01193 -3.87344 0.00000 3.96088 -4.50305 -2.10206 +TYR( 4) 7.87243 -3.87344 0.00000 10.79652 -4.89021 -1.22632 +ILE( 5) 7.89655 -1.17680 2.77774 7.76075 0.44675 2.31935 +GLN( 6) 5.70141 -3.47509 4.94285 3.60888 -3.02771 5.88565 +TRP( 7) 8.16996 -6.36206 4.22016 10.77228 -8.29798 2.61912 +LEU( 8) 11.25658 -4.20989 5.07405 12.42370 -3.38205 3.52958 +LYS( 9) 9.76612 -2.79308 8.36640 6.86736 -2.82804 9.12493 +ASP( 10) 9.49962 -6.42561 9.64741 7.69328 -7.25489 9.53489 +GLY( 11) 13.31647 -6.90493 9.06335 13.31647 -6.90493 9.06335 +GLY( 12) 13.30671 -8.01769 5.36352 13.30671 -8.01769 5.36352 +PRO( 13) 15.31165 -11.32992 5.02827 16.17763 -10.48298 4.32295 +SER( 14) 15.75414 -11.41497 8.87760 16.77305 -10.71800 9.16233 +SER( 15) 11.95328 -11.92981 9.42670 11.12717 -10.97987 9.51528 +GLY( 16) 11.45094 -15.53878 8.13618 11.45094 -15.53878 8.13618 +ARG( 17) 9.54906 -14.31220 5.00147 7.79760 -12.40573 7.22288 +PRO( 18) 10.53690 -13.94710 1.26956 9.62009 -14.99504 1.15440 +PRO( 19) 10.30439 -10.55356 -0.55592 11.52337 -10.99526 -1.06954 +PRO( 20) 6.99735 -9.68439 -2.34313 7.03150 -8.66136 -1.39345 +SER( 21) 7.20688 -9.78655 -6.20031 7.28380 -10.16020 -6.79638 +D ( 22) 3.89984 -8.91739 -7.98752 3.89984 -8.91739 -7.98752 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 -ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000 -LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000 -TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000 -ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000 -GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000 -TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000 -LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000 -LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000 -ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000 -GLY 11 3.800 90.000 180.000 0.000 180.000 180.000 -GLY 12 3.800 90.000 180.000 0.000 180.000 180.000 -PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000 -SER 14 3.800 90.000 180.000 1.150 110.000 -120.000 -SER 15 3.800 90.000 180.000 1.150 110.000 -120.000 -GLY 16 3.800 90.000 180.000 0.000 180.000 180.000 -ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000 -PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000 -PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000 -PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000 -SER 21 3.800 90.000 180.000 1.150 110.000 -120.000 -D 22 3.800 90.000 180.000 0.000 180.000 180.000 +ASN 2 3.861 0.000 0.000 1.977 94.624 -178.093 +LEU 3 3.876 92.239 0.000 2.195 102.878 -79.236 +TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440 +ILE 5 3.871 90.357 45.849 1.692 144.011 -104.516 +GLN 6 3.846 89.090 55.194 2.338 170.986 -139.318 +TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913 +LEU 8 3.859 93.032 48.298 2.105 151.723 -105.899 +LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960 +ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646 +GLY 11 3.891 89.908 56.679 0.000 180.000 180.000 +GLY 12 3.864 100.181 -87.304 0.000 180.000 180.000 +PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580 +SER 14 3.876 89.537 4.261 1.267 144.515 -129.218 +SER 15 3.875 91.815 66.108 1.262 161.047 -100.177 +GLY 16 3.866 101.784 70.140 0.000 180.000 180.000 +ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716 +PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024 +PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417 +PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207 +SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341 +D 22 3.858 114.201 180.000 0.000 180.000 180.000 Potential energy and its components Virtual-chain energies: -EVDW= -1.947821E+01 WEIGHT= 1.000000D+00 (SC-SC) -EVDW2= 2.387106E+01 WEIGHT= 1.233150D+00 (SC-p) -EES= -7.520330E+00 WEIGHT= 8.447600D-01 (p-p) -EVDWPP= -2.624923E+01 WEIGHT= 2.317300D-01 (p-p VDW) -ESTR= 1.118676E+02 WEIGHT= 1.000000D+00 (stretching) -EBE= -1.933948E+01 WEIGHT= 6.295400D-01 (bending) -ESC= 8.868295E+01 WEIGHT= 1.055400D-01 (SC local) -ETORS= 2.664535E-15 WEIGHT= 1.843160D+00 (torsional) -ETORSD= -2.547586E+00 WEIGHT= 1.265710D+00 (double torsional) +EVDW= -1.798849E+01 WEIGHT= 1.000000D+00 (SC-SC) +EVDW2= 4.471415E+01 WEIGHT= 1.233150D+00 (SC-p) +EES= -9.165378E+01 WEIGHT= 8.447600D-01 (p-p) +EVDWPP= -3.362882E+01 WEIGHT= 2.317300D-01 (p-p VDW) +ESTR= 5.659036E+01 WEIGHT= 1.000000D+00 (stretching) +EBE= -5.669935E+00 WEIGHT= 6.295400D-01 (bending) +ESC= 1.734458E+02 WEIGHT= 1.055400D-01 (SC local) +ETORS= 1.479510E+01 WEIGHT= 1.843160D+00 (torsional) +ETORSD= 1.006444E+00 WEIGHT= 1.265710D+00 (double torsional) EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) -ECORR4= -4.501075E+00 WEIGHT= 1.921200D-01 (multi-body) +ECORR4= -6.528803E+01 WEIGHT= 1.921200D-01 (multi-body) ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) -EELLO= 2.197932E+01 WEIGHT= 3.735700D-01 (electrostatic-local) -ETURN3= -1.258124E+00 WEIGHT= 1.403230D+00 (turns, 3rd order) -ETURN4= 9.498513E+00 WEIGHT= 6.467300D-01 (turns, 4th order) +EELLO= -4.012900E+00 WEIGHT= 3.735700D-01 (electrostatic-local) +ETURN3= 1.829789E+01 WEIGHT= 1.403230D+00 (turns, 3rd order) +ETURN4= 6.580750E-01 WEIGHT= 6.467300D-01 (turns, 4th order) ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order) ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+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= 1.150741E+02 (total) +ETOT= 6.386200E+01 (total) Initial: - Kinetic energy 3.16218E+01 - potential energy 1.15074E+02 - total energy 1.46696E+02 + Kinetic energy 3.07644E+01 + potential energy 6.38620E+01 + total energy 9.46264E+01 - maximum acceleration 4.85027E+00 + maximum acceleration 1.97191E+00 =================================== Timing =================================== MD calculations setup: 1.17188E-02 - Energy & gradient evaluation: 4.71867E+02 + Energy & gradient evaluation: 2.61488E+02 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 - MD steps: 5.30824E+02 + MD steps: 2.89031E+02 ============================ End of MD calculation =========================== CG processor 0 is finishing work. - Total wall clock time 541.898437500000 sec + Total wall clock time 289.093750000000 sec