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.1e0g-52-17k-2k-newclass-shan1e9_ga
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 Mon Jul 23 17:42:12 2012
35 compiled by jal47@matrix.chem.cornell.edu
37 OS release: 2.6.34.9-69.fc13.x86_64
38 OS version: #1 SMP Tue May 3 09:23:03 UTC 2011
40 INSTALL_DIR = /users/software/mpich-1.2.7p1_int...
43 FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
44 FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...
45 FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include
46 FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...
47 LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...
50 object = unres.o arcos.o cartprint.o chainbuild...
51 GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...
52 GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP...
53 E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...
54 E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...
55 ++++ End of compile info ++++
57 Potential is GB , exponents are 6 12
59 Disulfide bridge parameters:
60 S-S bridge energy: -5.50
61 d0cm: 3.78 akcm: 15.10
62 akth: 11.00 akct: 12.00
63 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
64 MPI: node= 0 iseed(4)= 0 0 -46
66 ran_num 6.422640197456531E-013
72 Time limit (min): 960.0
74 Library routine used to diagonalize matrices.
76 =========================== Parameters of the MD run ===========================
79 positions: angstrom, time: 48.9 fs
80 velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2
81 energy: kcal/mol, temperature: K
83 Number of time steps: 1000000
84 Initial time step of numerical integration: 0.01000 natural units
86 A-MTS algorithm used; initial time step for fast-varying short-range forces split into 1 steps.
87 Short-range force cutoff 2.00 lambda 0.30
88 Maximum acceleration threshold to reduce the time step/increase split number: 20.00000
89 Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000
90 Maximum velocity threshold to reduce velocities: 20.00000
91 Frequency of property output: 10000
92 Frequency of coordinate output: 10000
93 Microcanonical mode calculation
95 ============================== End of MD run setup =============================
98 Energy-term weights (unscaled):
100 WSCC= 1.352790 (SC-SC)
101 WSCP= 1.593040 (SC-p)
102 WELEC= 0.715340 (p-p electr)
103 WVDWPP= 0.113710 (p-p VDW)
104 WBOND= 1.000000 (stretching)
105 WANG= 1.138730 (bending)
106 WSCLOC= 0.162580 (SC local)
107 WTOR= 1.985990 (torsional)
108 WTORD= 1.570690 (double torsional)
109 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
110 WEL_LOC= 0.160360 (multi-body 3-rd order)
111 WCORR4= 0.428870 (multi-body 4th order)
112 WCORR5= 0.000000 (multi-body 5th order)
113 WCORR6= 0.000000 (multi-body 6th order)
114 WSCCOR= 0.000000 (back-scloc correlation)
115 WTURN3= 1.687220 (turns, 3rd order)
116 WTURN4= 0.662300 (turns, 4th order)
117 WTURN6= 0.000000 (turns, 6th order)
119 Hydrogen-bonding correlation between contact pairs of peptide groups
121 Scaling factor of 1,4 SC-p interactions: 0.400
122 General scaling factor of SC-p interactions: 1.000
124 Energy-term weights (scaled):
126 WSCC= 1.352790 (SC-SC)
127 WSCP= 1.593040 (SC-p)
128 WELEC= 0.715340 (p-p electr)
129 WVDWPP= 0.113710 (p-p VDW)
130 WBOND= 1.000000 (stretching)
131 WANG= 1.138730 (bending)
132 WSCLOC= 0.162580 (SC local)
133 WTOR= 1.985990 (torsional)
134 WTORD= 1.570690 (double torsional)
135 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
136 WEL_LOC= 0.160360 (multi-body 3-rd order)
137 WCORR4= 0.428870 (multi-body 4th order)
138 WCORR5= 0.000000 (multi-body 5th order)
139 WCORR6= 0.000000 (multi-body 6th order)
140 WSCCOR= 0.000000 (back-scloc correlatkion)
141 WTURN3= 1.687220 (turns, 3rd order)
142 WTURN4= 0.662300 (turns, 4th order)
143 WTURN6= 0.000000 (turns, 6th order)
144 Reference temperature for weights calculation: 300.000000000000
145 Parameters of the SS-bond potential:
146 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
147 11.0000000000000 AKCT 12.0000000000000
148 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
150 EBR -5.50000000000000
151 PDB data will be read from file ../../../1L2Y.pdb
153 Backbone and SC coordinates as read from the PDB
154 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
155 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
156 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
157 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
158 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
159 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
160 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
161 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
162 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
163 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
164 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
165 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
166 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
167 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
168 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
169 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
170 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
171 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
172 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
173 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
174 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
175 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
176 nsup= 20 nstart_sup= 2
200 Boundaries in phi angle sampling:
224 nsup= 20 nstart_sup= 2 nstart_seq= 2
225 NZ_START= 2 NZ_END= 21
227 Contact order: 0.308441558441558
228 Shifting contacts: 2 2
243 Initial geometry will be read in.
245 Geometry of the virtual chain.
246 Res d Theta Gamma Dsc Alpha Beta
247 D 1 0.000 0.000 0.000 0.000 0.000 0.000
248 ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317
249 LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685
250 TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090
251 ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666
252 GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945
253 TRP 7 3.800 84.466 51.434 2.605 152.178 38.024
254 LEU 8 3.800 83.945 53.508 1.939 159.052 179.471
255 LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090
256 ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797
257 GLY 11 3.800 94.602 67.604 0.000 0.000 0.000
258 GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000
259 PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163
260 SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659
261 SER 15 3.800 96.264 67.358 1.150 146.290 -130.305
262 GLY 16 3.800 138.119 129.701 0.000 0.000 0.000
263 ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747
264 PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641
265 PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044
266 PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374
267 SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303
268 D 22 3.800 108.718 92.113 0.000 0.000 0.000
271 ********************************************************************************
272 Processor 0: end reading molecular data.
273 ********************************************************************************
276 Mesoscopic molecular dynamics (MD) calculation.
278 ********************************************************************************
281 ====================MD calculation start====================
282 Initial velocities randomly generated
284 0 0.02267 0.06282 -0.18129 0.00000 0.00000 0.00000
285 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
286 2 -0.36014 -0.22705 -0.00171 -0.06904 -0.02446 0.24778
287 3 0.27655 0.20645 0.14150 0.26200 0.15105 0.09342
288 4 0.10834 -0.11941 0.14712 0.10330 -0.09595 0.03277
289 5 0.05798 -0.08974 0.08325 0.03879 0.02648 -0.14707
290 6 0.01211 0.16444 -0.14711 -0.01628 0.11599 -0.16511
291 7 -0.01010 -0.05513 0.03662 -0.18958 0.06429 0.04531
292 8 -0.01799 0.13439 -0.04510 0.02318 0.10657 0.03722
293 9 -0.26458 -0.01929 0.09531 -0.22533 -0.17075 -0.04594
294 10 0.14062 -0.06051 -0.18363 0.20415 -0.15549 -0.17329
295 11 -0.14145 0.13159 -0.00733 0.00000 0.00000 0.00000
296 12 0.19745 -0.24261 0.01759 0.00000 0.00000 0.00000
297 13 -0.15305 0.28008 0.07251 0.06558 0.14824 0.10057
298 14 0.11104 -0.31941 0.15684 -0.02949 -0.09688 0.05398
299 15 0.14534 0.10342 -0.23754 -0.13923 0.07952 0.07655
300 16 -0.11969 0.14757 0.15002 0.00000 0.00000 0.00000
301 17 -0.09007 -0.15856 -0.20234 -0.07955 -0.08516 -0.10245
302 18 0.24139 0.09063 0.14043 -0.02074 0.10220 0.04907
303 19 -0.14354 -0.07226 -0.29143 -0.12408 -0.06855 -0.02978
304 20 0.28536 0.09023 0.56577 0.02348 0.16297 0.19270
305 21 0.00000 0.00000 0.00000 -0.13725 -0.06434 -0.21957
306 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
307 Calling the zero-angular momentum subroutine
308 vcm right after adjustment:
309 7.350442094070002E-018 -1.983088023295969E-017 2.245968417632500E-018
312 alpha-carbon coordinates centroid coordinates
314 D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
315 ASN( 2) 3.80000 0.00000 0.00000 4.19395 0.15176 1.63022
316 LEU( 3) 4.77894 -3.67174 0.00000 6.45470 -4.61120 -0.26262
317 TYR( 4) 5.40376 -3.34701 3.73419 6.99608 -4.40943 5.31723
318 ILE( 5) 1.60715 -3.20688 3.81267 0.66846 -2.00631 2.90072
319 GLN( 6) 1.94839 -6.79081 2.59652 1.67496 -6.00460 0.51692
320 TRP( 7) 4.28674 -7.18710 5.56554 6.06986 -8.42183 7.00843
321 LEU( 8) 1.35234 -5.80840 7.54758 1.66208 -4.14953 8.50254
322 LYS( 9) -0.53224 -8.86183 6.29662 0.02805 -9.25716 3.84989
323 ASP( 10) 2.43549 -11.11658 7.03737 3.20275 -10.98938 5.51559
324 GLY( 11) 2.18504 -10.72111 10.80843 2.18504 -10.72111 10.80843
325 GLY( 12) 3.43786 -7.16826 11.30614 3.43786 -7.16826 11.30614
326 PRO( 13) 6.99461 -6.28836 10.29851 6.42185 -5.11686 9.96902
327 SER( 14) 8.57536 -7.97729 13.31326 8.31540 -7.39705 14.27151
328 SER( 15) 7.65918 -11.53050 12.32568 6.78456 -11.09058 11.72234
329 GLY( 16) 9.38152 -14.89751 11.95581 9.38152 -14.89751 11.95581
330 ARG( 17) 10.03694 -14.62275 8.22286 7.37409 -13.20714 8.38321
331 PRO( 18) 12.21420 -12.16088 6.31531 11.85460 -12.99540 5.32369
332 PRO( 19) 10.48638 -8.77881 6.18806 11.49173 -8.46972 7.02636
333 PRO( 20) 10.10763 -7.90895 2.50840 8.81244 -7.79183 2.85161
334 SER( 21) 11.17729 -4.27813 2.17220 10.31507 -3.69519 2.66134
335 D ( 22) 14.88269 -4.17086 1.33644 14.88269 -4.17086 1.33644
337 Geometry of the virtual chain.
338 Res d Theta Gamma Dsc Alpha Beta
339 D 1 0.000 0.000 0.000 0.000 0.000 0.000
340 ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317
341 LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685
342 TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090
343 ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666
344 GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945
345 TRP 7 3.800 84.466 51.434 2.605 152.178 38.024
346 LEU 8 3.800 83.945 53.508 1.939 159.052 179.471
347 LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090
348 ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797
349 GLY 11 3.800 94.602 67.604 0.000 180.000 180.000
350 GLY 12 3.800 101.862 -72.814 0.000 180.000 180.000
351 PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163
352 SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659
353 SER 15 3.800 96.264 67.358 1.150 146.290 -130.306
354 GLY 16 3.800 138.119 129.701 0.000 180.000 180.000
355 ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747
356 PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641
357 PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.045
358 PRO 20 3.800 106.349 -122.306 1.345 93.777 -102.374
359 SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303
360 D 22 3.800 108.718 92.113 0.000 180.000 180.000
361 Potential energy and its components
363 Virtual-chain energies:
365 EVDW= -4.436790E+01 WEIGHT= 1.352790D+00 (SC-SC)
366 EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p)
367 EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p)
368 EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW)
369 ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
370 EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending)
371 ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local)
372 ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional)
373 ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional)
374 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
375 ECORR4= -8.338619E+01 WEIGHT= 4.288700D-01 (multi-body)
376 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
377 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
378 EELLO= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
379 ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
380 ETURN4= -7.304754E+00 WEIGHT= 6.623000D-01 (turns, 4th order)
381 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
382 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
383 EDIHC= 0.000000E+00 (dihedral angle constraints)
384 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
385 UCONST= 0.000000E+00 (Constraint energy)
386 ETOT= -5.145065E+01 (total)
389 Kinetic energy 3.24616E+01
390 potential energy -5.14506E+01
391 total energy -1.89891E+01
393 maximum acceleration 1.98994E-01
397 =================================== Timing ===================================
399 MD calculations setup: 3.90625E-03
400 Energy & gradient evaluation: 3.78512E+02
401 Stochastic MD setup: 0.00000E+00
402 Stochastic MD step setup: 0.00000E+00
403 MD steps: 4.12785E+02
406 ============================ End of MD calculation ===========================
407 CG processor 0 is finishing work.
408 Total wall clock time 419.316406250000 sec