1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1L2Y_micro.inp
5 Output file : 1L2Y_micro.out_GB000
7 Sidechain potential file :
8 /users/pk376/unres-git/unres/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-1
10 SCp potential file : /users/pk376/unres-git/unres/PARAM/scp.parm
11 Electrostatic potential file :
12 /users/pk376/unres-git/unres/PARAM/electr_631Gdp.parm
13 Cumulant coefficient file :
14 /users/pk376/unres-git/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3
15 Torsional parameter file :
16 /users/pk376/unres-git/unres/PARAM/torsion_631Gdp.parm
17 Double torsional parameter file :
18 /users/pk376/unres-git/unres/PARAM/torsion_double_631Gdp.parm
19 SCCOR parameter file : /users/pk376/unres-git/unres/PARAM/sccor_pdb_shelly.dat
20 Bond & inertia constant file : /users/pk376/unres-git/unres/PARAM/bond.parm
21 Bending parameter file :
22 /users/pk376/unres-git/unres/PARAM/thetaml.5parm
23 Rotamer parameter file :
24 /users/pk376/unres-git/unres/PARAM/scgauss.parm
26 /users/pk376/unres-git/unres/PARAM/patterns.cart
27 --------------------------------------------------------------------------------
28 ********************************************************************************
29 United-residue force field calculation - parallel job.
30 ********************************************************************************
31 ### LAST MODIFIED 03/28/12 23:29 by czarek
32 ++++ Compile info ++++
34 Compiled Wed Nov 20 08:38:19 EST 2013
35 Compiled by pk376@matrix.chem.cornell.edu
37 OS release: Linux-2.6.34.9-69.fc13.x86_64
38 Fortran Compiler: /opt/intel/Compiler/11.1/046/bin
41 CPPFLAGS = PROCOR -DUNRES -DISNAN -DSPLITELE -DLAN
42 G0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DLINUX
44 ++++ End of compile info ++++
46 Potential is GB , exponents are 6 12
48 Disulfide bridge parameters:
49 S-S bridge energy: -5.50
50 d0cm: 3.78 akcm: 15.10
51 akth: 11.00 akct: 12.00
52 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
53 MPI: node= 0 iseed(4)= 0 0 -46
55 ran_num 6.422640197456531E-013
61 Time limit (min): 960.0
63 Library routine used to diagonalize matrices.
65 =========================== Parameters of the MD run ===========================
68 positions: angstrom, time: 48.9 fs
69 velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2
70 energy: kcal/mol, temperature: K
72 Number of time steps: 1000000
73 Initial time step of numerical integration: 0.01000 natural units
75 A-MTS algorithm used; initial time step for fast-varying short-range forces split into 1 steps.
76 Short-range force cutoff 2.00 lambda 0.30
77 Maximum acceleration threshold to reduce the time step/increase split number: 20.00000
78 Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000
79 Maximum velocity threshold to reduce velocities: 20.00000
80 Frequency of property output: 10000
81 Frequency of coordinate output: 10000
82 Microcanonical mode calculation
84 ============================== End of MD run setup =============================
87 Energy-term weights (unscaled):
89 WSCC= 1.352790 (SC-SC)
91 WELEC= 0.715340 (p-p electr)
92 WVDWPP= 0.113710 (p-p VDW)
93 WBOND= 1.000000 (stretching)
94 WANG= 1.138730 (bending)
95 WSCLOC= 0.162580 (SC local)
96 WTOR= 1.985990 (torsional)
97 WTORD= 1.570690 (double torsional)
98 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
99 WEL_LOC= 0.160360 (multi-body 3-rd order)
100 WCORR4= 0.428870 (multi-body 4th order)
101 WCORR5= 0.000000 (multi-body 5th order)
102 WCORR6= 0.000000 (multi-body 6th order)
103 WSCCOR= 0.000000 (back-scloc correlation)
104 WTURN3= 1.687220 (turns, 3rd order)
105 WTURN4= 0.662300 (turns, 4th order)
106 WTURN6= 0.000000 (turns, 6th order)
108 Hydrogen-bonding correlation between contact pairs of peptide groups
110 Scaling factor of 1,4 SC-p interactions: 0.400
111 General scaling factor of SC-p interactions: 1.000
113 Energy-term weights (scaled):
115 WSCC= 1.352790 (SC-SC)
116 WSCP= 1.593040 (SC-p)
117 WELEC= 0.715340 (p-p electr)
118 WVDWPP= 0.113710 (p-p VDW)
119 WBOND= 1.000000 (stretching)
120 WANG= 1.138730 (bending)
121 WSCLOC= 0.162580 (SC local)
122 WTOR= 1.985990 (torsional)
123 WTORD= 1.570690 (double torsional)
124 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
125 WEL_LOC= 0.160360 (multi-body 3-rd order)
126 WCORR4= 0.428870 (multi-body 4th order)
127 WCORR5= 0.000000 (multi-body 5th order)
128 WCORR6= 0.000000 (multi-body 6th order)
129 WSCCOR= 0.000000 (back-scloc correlatkion)
130 WTURN3= 1.687220 (turns, 3rd order)
131 WTURN4= 0.662300 (turns, 4th order)
132 WTURN6= 0.000000 (turns, 6th order)
133 Reference temperature for weights calculation: 300.000000000000
134 Parameters of the SS-bond potential:
135 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
136 11.0000000000000 AKCT 12.0000000000000
137 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
139 EBR -5.50000000000000 SS_DEPTH -7.39571661678271
140 HT 0.000000000000000E+000
141 PDB data will be read from file ../../../../1L2Y.pdb
143 Backbone and SC coordinates as read from the PDB
144 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
145 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
146 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
147 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
148 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
149 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
150 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
151 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
152 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
153 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
154 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
155 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
156 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
157 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
158 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
159 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
160 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
161 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
162 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
163 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
164 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
165 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
166 nsup= 20 nstart_sup= 2
190 Boundaries in phi angle sampling:
214 nsup= 20 nstart_sup= 2 nstart_seq= 2
215 NZ_START= 2 NZ_END= 21
217 Contact order: 0.308441558441558
218 Shifting contacts: 2 2
233 Initial geometry will be read in.
235 Geometry of the virtual chain.
236 Res d Theta Gamma Dsc Alpha Beta
237 D 1 0.000 0.000 0.000 0.000 0.000 0.000
238 ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317
239 LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685
240 TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090
241 ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666
242 GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945
243 TRP 7 3.800 84.466 51.434 2.605 152.178 38.024
244 LEU 8 3.800 83.945 53.508 1.939 159.052 179.471
245 LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090
246 ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797
247 GLY 11 3.800 94.602 67.604 0.000 0.000 0.000
248 GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000
249 PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163
250 SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659
251 SER 15 3.800 96.264 67.358 1.150 146.290 -130.305
252 GLY 16 3.800 138.119 129.701 0.000 0.000 0.000
253 ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747
254 PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641
255 PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044
256 PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374
257 SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303
258 D 22 3.800 108.718 92.113 0.000 0.000 0.000
261 ********************************************************************************
262 Processor 0: end reading molecular data.
263 ********************************************************************************
266 Mesoscopic molecular dynamics (MD) calculation.
268 ********************************************************************************
271 ====================MD calculation start====================
272 Initial velocities randomly generated
274 0 0.02267 0.06282 -0.18129 0.00000 0.00000 0.00000
275 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
276 2 -0.36014 -0.22705 -0.00171 -0.06904 -0.02446 0.24778
277 3 0.27655 0.20645 0.14150 0.26200 0.15105 0.09342
278 4 0.10834 -0.11941 0.14712 0.10330 -0.09595 0.03277
279 5 0.05798 -0.08974 0.08325 0.03879 0.02648 -0.14707
280 6 0.01211 0.16444 -0.14711 -0.01628 0.11599 -0.16511
281 7 -0.01010 -0.05513 0.03662 -0.18958 0.06429 0.04531
282 8 -0.01799 0.13439 -0.04510 0.02318 0.10657 0.03722
283 9 -0.26458 -0.01929 0.09531 -0.22533 -0.17075 -0.04594
284 10 0.14062 -0.06051 -0.18363 0.20415 -0.15549 -0.17329
285 11 -0.14145 0.13159 -0.00733 0.00000 0.00000 0.00000
286 12 0.19745 -0.24261 0.01759 0.00000 0.00000 0.00000
287 13 -0.15305 0.28008 0.07251 0.06558 0.14824 0.10057
288 14 0.11104 -0.31941 0.15684 -0.02949 -0.09688 0.05398
289 15 0.14534 0.10342 -0.23754 -0.13923 0.07952 0.07655
290 16 -0.11969 0.14757 0.15002 0.00000 0.00000 0.00000
291 17 -0.09007 -0.15856 -0.20234 -0.07955 -0.08516 -0.10245
292 18 0.24139 0.09063 0.14043 -0.02074 0.10220 0.04907
293 19 -0.14354 -0.07226 -0.29143 -0.12408 -0.06855 -0.02978
294 20 0.28536 0.09023 0.56577 0.02348 0.16297 0.19270
295 21 0.00000 0.00000 0.00000 -0.13725 -0.06434 -0.21957
296 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
297 Calling the zero-angular momentum subroutine
298 vcm right after adjustment:
299 2.450147364690000E-018 3.126490126817969E-017 6.737905252897502E-018
302 alpha-carbon coordinates centroid coordinates
304 D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
305 ASN( 2) 3.80000 0.00000 0.00000 4.19395 0.15176 1.63022
306 LEU( 3) 4.77894 -3.67174 0.00000 6.45470 -4.61120 -0.26262
307 TYR( 4) 5.40376 -3.34701 3.73419 6.99608 -4.40943 5.31723
308 ILE( 5) 1.60715 -3.20688 3.81267 0.66846 -2.00631 2.90072
309 GLN( 6) 1.94839 -6.79081 2.59652 1.67496 -6.00460 0.51692
310 TRP( 7) 4.28674 -7.18710 5.56554 6.06986 -8.42183 7.00843
311 LEU( 8) 1.35234 -5.80840 7.54758 1.66208 -4.14953 8.50254
312 LYS( 9) -0.53224 -8.86183 6.29662 0.02805 -9.25716 3.84989
313 ASP( 10) 2.43549 -11.11658 7.03737 3.20275 -10.98938 5.51559
314 GLY( 11) 2.18504 -10.72111 10.80843 2.18504 -10.72111 10.80843
315 GLY( 12) 3.43786 -7.16826 11.30614 3.43786 -7.16826 11.30614
316 PRO( 13) 6.99461 -6.28836 10.29851 6.42185 -5.11686 9.96902
317 SER( 14) 8.57536 -7.97729 13.31326 8.31540 -7.39705 14.27151
318 SER( 15) 7.65918 -11.53050 12.32568 6.78456 -11.09058 11.72234
319 GLY( 16) 9.38152 -14.89751 11.95581 9.38152 -14.89751 11.95581
320 ARG( 17) 10.03694 -14.62275 8.22286 7.37409 -13.20714 8.38321
321 PRO( 18) 12.21420 -12.16088 6.31531 11.85460 -12.99540 5.32369
322 PRO( 19) 10.48638 -8.77881 6.18806 11.49173 -8.46972 7.02636
323 PRO( 20) 10.10763 -7.90895 2.50840 8.81244 -7.79183 2.85161
324 SER( 21) 11.17729 -4.27813 2.17220 10.31507 -3.69519 2.66134
325 D ( 22) 14.88269 -4.17086 1.33644 14.88269 -4.17086 1.33644
327 Geometry of the virtual chain.
328 Res d Theta Gamma Dsc Alpha Beta
329 D 1 0.000 0.000 0.000 0.000 0.000 0.000
330 ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317
331 LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685
332 TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090
333 ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666
334 GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945
335 TRP 7 3.800 84.466 51.434 2.605 152.178 38.024
336 LEU 8 3.800 83.945 53.508 1.939 159.052 179.471
337 LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090
338 ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797
339 GLY 11 3.800 94.602 67.604 0.000 0.000 180.000
340 GLY 12 3.800 101.862 -72.814 0.000 0.000 180.000
341 PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163
342 SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659
343 SER 15 3.800 96.264 67.358 1.150 146.290 -130.306
344 GLY 16 3.800 138.119 129.701 0.000 0.000 180.000
345 ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747
346 PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641
347 PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.045
348 PRO 20 3.800 106.349 -122.306 1.345 93.777 -102.374
349 SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303
350 D 22 3.800 108.718 92.113 0.000 0.000 180.000
351 Potential energy and its components
353 Virtual-chain energies:
355 EVDW= -4.954316E+01 WEIGHT= 1.352790E+00 (SC-SC)
356 EVDW2= 5.228224E+01 WEIGHT= 1.593040E+00 (SC-p)
357 EES= -1.132072E+02 WEIGHT= 7.153400E-01 (p-p)
358 EVDWPP= 2.375178E+01 WEIGHT= 1.137100E-01 (p-p VDW)
359 ESTR= 6.779273E-27 WEIGHT= 1.000000E+00 (stretching)
360 EBE= -1.651995E+01 WEIGHT= 1.138730E+00 (bending)
361 ESC= 7.185904E+01 WEIGHT= 1.625800E-01 (SC local)
362 ETORS= 8.243370E+00 WEIGHT= 1.985990E+00 (torsional)
363 ETORSD= 2.390466E+00 WEIGHT= 1.570690E+00 (double torsional)
364 EHPB= 0.000000E+00 WEIGHT= 1.000000E+00 (SS bridges & dist. cnstr.)
365 ECORR4= -8.338619E+01 WEIGHT= 4.288700E-01 (multi-body)
366 ECORR5= 0.000000E+00 WEIGHT= 0.000000E+00 (multi-body)
367 ECORR6= 0.000000E+00 WEIGHT= 0.000000E+00 (multi-body)
368 EELLO= -5.753258E+00 WEIGHT= 1.603600E-01 (electrostatic-local)
369 ETURN3= 1.901845E+01 WEIGHT= 1.687220E+00 (turns, 3rd order)
370 ETURN4= -7.304754E+00 WEIGHT= 6.623000E-01 (turns, 4th order)
371 ETURN6= 0.000000E+00 WEIGHT= 0.000000E+00 (turns, 6th order)
372 ESCCOR= 0.000000E+00 WEIGHT= 0.000000E+00 (backbone-rotamer corr)
373 EDIHC= 0.000000E+00 (dihedral angle constraints)
374 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
375 UCONST= 0.000000E+00 (Constraint energy)
376 ETOT= -5.845168E+01 (total)
379 Kinetic energy 3.24616E+01
380 potential energy -5.84517E+01
381 total energy -2.59901E+01
383 maximum acceleration 2.04223E-01
387 =================================== Timing ===================================
389 MD calculations setup: 3.90625E-03
390 Energy & gradient evaluation: 3.39035E+02
391 Stochastic MD setup: 0.00000E+00
392 Stochastic MD step setup: 0.00000E+00
393 MD steps: 3.59645E+02
396 ============================ End of MD calculation ===========================
397 CG processor 0 is finishing work.
398 Total wall clock time 364.515625000000 sec