Output file : 1L2Y_micro.out_GB000
Sidechain potential file :
- /users/aks255/newUNRES/unres/PARAM/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_ga
+ /users/pk376/unres-git/unres/PARAM/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_ga
p8g-sc
- SCp potential file : /users/aks255/newUNRES/unres/PARAM/scp.parm
+ SCp potential file : /users/pk376/unres-git/unres/PARAM/scp.parm
Electrostatic potential file :
- /users/aks255/newUNRES/unres/PARAM/electr_631Gdp.parm
+ /users/pk376/unres-git/unres/PARAM/electr_631Gdp.parm
Cumulant coefficient file :
- /users/aks255/newUNRES/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3
+ /users/pk376/unres-git/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3
Torsional parameter file :
- /users/aks255/newUNRES/unres/PARAM/torsion_631Gdp.parm
+ /users/pk376/unres-git/unres/PARAM/torsion_631Gdp.parm
Double torsional parameter file :
- /users/aks255/newUNRES/unres/PARAM/torsion_double_631Gdp.parm
- SCCOR parameter file : /users/aks255/newUNRES/unres/PARAM/sccor_pdb_shelly.dat
- Bond & inertia constant file : /users/aks255/newUNRES/unres/PARAM/bond.parm
+ /users/pk376/unres-git/unres/PARAM/torsion_double_631Gdp.parm
+ SCCOR parameter file : /users/pk376/unres-git/unres/PARAM/sccor_pdb_shelly.dat
+ Bond & inertia constant file : /users/pk376/unres-git/unres/PARAM/bond.parm
Bending parameter file :
- /users/aks255/newUNRES/unres/PARAM/thetaml.5parm
+ /users/pk376/unres-git/unres/PARAM/thetaml.5parm
Rotamer parameter file :
- /users/aks255/newUNRES/unres/PARAM/scgauss.parm
+ /users/pk376/unres-git/unres/PARAM/scgauss.parm
Threading database :
- /users/aks255/newUNRES/unres/PARAM/patterns.cart
+ /users/pk376/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 2.5 build 300
- compiled Thu Jul 5 03:59:46 2012
- compiled by aks255@matrix.chem.cornell.edu
+ Version 2.5 build 302
+ compiled Mon Jul 23 17:42:12 2012
+ compiled by jal47@matrix.chem.cornell.edu
OS name: Linux
OS release: 2.6.34.9-69.fc13.x86_64
OS version: #1 SMP Tue May 3 09:23:03 UTC 2011
12 PRO 20 LEU 3
13 PRO 20 TYR 4
14 PRO 20 TRP 7
+Initial geometry will be read in.
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 3.861 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
+ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317
+LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685
+TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090
+ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666
+GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945
+TRP 7 3.800 84.466 51.434 2.605 152.178 38.024
+LEU 8 3.800 83.945 53.508 1.939 159.052 179.471
+LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090
+ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797
+GLY 11 3.800 94.602 67.604 0.000 0.000 0.000
+GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000
+PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163
+SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659
+SER 15 3.800 96.264 67.358 1.150 146.290 -130.305
+GLY 16 3.800 138.119 129.701 0.000 0.000 0.000
+ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747
+PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641
+PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044
+PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374
+SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303
+D 22 3.800 108.718 92.113 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:
- 4.226504204090251E-017 -1.020894735287500E-018 -4.083578941150001E-019
+ 7.350442094070002E-018 -1.983088023295969E-017 2.245968417632500E-018
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) 3.86050 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
+ASN( 2) 3.80000 0.00000 0.00000 4.19395 0.15176 1.63022
+LEU( 3) 4.77894 -3.67174 0.00000 6.45470 -4.61120 -0.26262
+TYR( 4) 5.40376 -3.34701 3.73419 6.99608 -4.40943 5.31723
+ILE( 5) 1.60715 -3.20688 3.81267 0.66846 -2.00631 2.90072
+GLN( 6) 1.94839 -6.79081 2.59652 1.67496 -6.00460 0.51692
+TRP( 7) 4.28674 -7.18710 5.56554 6.06986 -8.42183 7.00843
+LEU( 8) 1.35234 -5.80840 7.54758 1.66208 -4.14953 8.50254
+LYS( 9) -0.53224 -8.86183 6.29662 0.02805 -9.25716 3.84989
+ASP( 10) 2.43549 -11.11658 7.03737 3.20275 -10.98938 5.51559
+GLY( 11) 2.18504 -10.72111 10.80843 2.18504 -10.72111 10.80843
+GLY( 12) 3.43786 -7.16826 11.30614 3.43786 -7.16826 11.30614
+PRO( 13) 6.99461 -6.28836 10.29851 6.42185 -5.11686 9.96902
+SER( 14) 8.57536 -7.97729 13.31326 8.31540 -7.39705 14.27151
+SER( 15) 7.65918 -11.53050 12.32568 6.78456 -11.09058 11.72234
+GLY( 16) 9.38152 -14.89751 11.95581 9.38152 -14.89751 11.95581
+ARG( 17) 10.03694 -14.62275 8.22286 7.37409 -13.20714 8.38321
+PRO( 18) 12.21420 -12.16088 6.31531 11.85460 -12.99540 5.32369
+PRO( 19) 10.48638 -8.77881 6.18806 11.49173 -8.46972 7.02636
+PRO( 20) 10.10763 -7.90895 2.50840 8.81244 -7.79183 2.85161
+SER( 21) 11.17729 -4.27813 2.17220 10.31507 -3.69519 2.66134
+D ( 22) 14.88269 -4.17086 1.33644 14.88269 -4.17086 1.33644
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 3.861 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
+ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317
+LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685
+TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090
+ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666
+GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945
+TRP 7 3.800 84.466 51.434 2.605 152.178 38.024
+LEU 8 3.800 83.945 53.508 1.939 159.052 179.471
+LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090
+ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797
+GLY 11 3.800 94.602 67.604 0.000 180.000 180.000
+GLY 12 3.800 101.862 -72.814 0.000 180.000 180.000
+PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163
+SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659
+SER 15 3.800 96.264 67.358 1.150 146.290 -130.306
+GLY 16 3.800 138.119 129.701 0.000 180.000 180.000
+ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747
+PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641
+PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.045
+PRO 20 3.800 106.349 -122.306 1.345 93.777 -102.374
+SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303
+D 22 3.800 108.718 92.113 0.000 180.000 180.000
Potential energy and its components
Virtual-chain energies:
-EVDW= -1.475487E+01 WEIGHT= 1.352790D+00 (SC-SC)
-EVDW2= 4.471415E+01 WEIGHT= 1.593040D+00 (SC-p)
-EES= -9.165378E+01 WEIGHT= 7.153400D-01 (p-p)
-EVDWPP= -3.362882E+01 WEIGHT= 1.137100D-01 (p-p VDW)
-ESTR= 6.750243E+02 WEIGHT= 1.000000D+00 (stretching)
-EBE= -3.261471E+01 WEIGHT= 1.138730D+00 (bending)
-ESC= 5.789477E+01 WEIGHT= 1.625800D-01 (SC local)
-ETORS= 1.479510E+01 WEIGHT= 1.985990D+00 (torsional)
-ETORSD= 1.006444E+00 WEIGHT= 1.570690D+00 (double torsional)
+EVDW= -4.436790E+01 WEIGHT= 1.352790D+00 (SC-SC)
+EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p)
+EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p)
+EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW)
+ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
+EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending)
+ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local)
+ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional)
+ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional)
EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
-ECORR4= -6.528803E+01 WEIGHT= 4.288700D-01 (multi-body)
+ECORR4= -8.338619E+01 WEIGHT= 4.288700D-01 (multi-body)
ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
-EELLO= -4.012900E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
-ETURN3= 1.829789E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
-ETURN4= 6.580750E-01 WEIGHT= 6.623000D-01 (turns, 4th order)
+EELLO= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
+ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
+ETURN4= -7.304754E+00 WEIGHT= 6.623000D-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= 6.628097E+02 (total)
+ETOT= -5.145065E+01 (total)
Initial:
- Kinetic energy 3.07644E+01
- potential energy 6.62810E+02
- total energy 6.93574E+02
+ Kinetic energy 3.24616E+01
+ potential energy -5.14506E+01
+ total energy -1.89891E+01
- maximum acceleration 8.66045E+00
+ maximum acceleration 1.98994E-01
=================================== Timing ===================================
- MD calculations setup: 1.17188E-02
- Energy & gradient evaluation: 2.48965E+02
+ MD calculations setup: 7.81250E-03
+ Energy & gradient evaluation: 2.64738E+02
Stochastic MD setup: 0.00000E+00
Stochastic MD step setup: 0.00000E+00
- MD steps: 2.76316E+02
+ MD steps: 2.96723E+02
============================ End of MD calculation ===========================
CG processor 0 is finishing work.
- Total wall clock time 278.832031250000 sec
+ Total wall clock time 298.832031250000 sec
projects / unres.git / blobdiff