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
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
********************************************************************************
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
projects / unres.git / blobdiff