1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
5 Output file : small.out_GB000
7 Sidechain potential file :
8 /users/czarek/UNRES/GIT/unres/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-
10 SCp potential file : /users/czarek/UNRES/GIT/unres/PARAM/scp.parm
11 Electrostatic potential file :
12 /users/czarek/UNRES/GIT/unres/PARAM/electr_631Gdp.parm
13 Cumulant coefficient file :
14 /users/czarek/UNRES/GIT/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3
15 Torsional parameter file :
16 /users/czarek/UNRES/GIT/unres/PARAM/torsion_631Gdp.parm
17 Double torsional parameter file :
18 /users/czarek/UNRES/GIT/unres/PARAM/torsion_double_631Gdp.parm
19 SCCOR parameter file : /users/czarek/UNRES/GIT/unres/PARAM/sccor_pdb_shelly.dat
20 Bond & inertia constant file : /users/czarek/UNRES/GIT/unres/PARAM/bond.parm
21 Bending parameter file :
22 /users/czarek/UNRES/GIT/unres/PARAM/thetaml.5parm
23 Rotamer parameter file :
24 /users/czarek/UNRES/GIT/unres/PARAM/scgauss.parm
26 /users/czarek/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 Fri Feb 15 13:06:59 2013
35 compiled by czarek@piasek3
37 OS release: 2.6.32-42-generic
38 OS version: #96-Ubuntu SMP Wed Aug 15 19:37:37 UTC 2012
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 -16
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: 100000
84 Initial time step of numerical integration: 0.01000 natural units
86 Maximum acceleration threshold to reduce the time step/increase split number: 5.00000
87 Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000
88 Maximum velocity threshold to reduce velocities: 20.00000
89 Frequency of property output: 100
90 Frequency of coordinate output: 500
91 Microcanonical mode calculation
93 ============================== End of MD run setup =============================
96 Energy-term weights (unscaled):
98 WSCC= 1.352790 (SC-SC)
100 WELEC= 0.715340 (p-p electr)
101 WVDWPP= 0.113710 (p-p VDW)
102 WBOND= 1.000000 (stretching)
103 WANG= 1.138730 (bending)
104 WSCLOC= 0.162580 (SC local)
105 WTOR= 1.985990 (torsional)
106 WTORD= 1.570690 (double torsional)
107 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
108 WEL_LOC= 0.160360 (multi-body 3-rd order)
109 WCORR4= 0.428870 (multi-body 4th order)
110 WCORR5= 0.000000 (multi-body 5th order)
111 WCORR6= 0.000000 (multi-body 6th order)
112 WSCCOR= 0.000000 (back-scloc correlation)
113 WTURN3= 1.687220 (turns, 3rd order)
114 WTURN4= 0.662300 (turns, 4th order)
115 WTURN6= 0.000000 (turns, 6th order)
117 Hydrogen-bonding correlation between contact pairs of peptide groups
119 Scaling factor of 1,4 SC-p interactions: 0.400
120 General scaling factor of SC-p interactions: 1.000
122 Energy-term weights (scaled):
124 WSCC= 1.352790 (SC-SC)
125 WSCP= 1.593040 (SC-p)
126 WELEC= 0.715340 (p-p electr)
127 WVDWPP= 0.113710 (p-p VDW)
128 WBOND= 1.000000 (stretching)
129 WANG= 1.138730 (bending)
130 WSCLOC= 0.162580 (SC local)
131 WTOR= 1.985990 (torsional)
132 WTORD= 1.570690 (double torsional)
133 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
134 WEL_LOC= 0.160360 (multi-body 3-rd order)
135 WCORR4= 0.428870 (multi-body 4th order)
136 WCORR5= 0.000000 (multi-body 5th order)
137 WCORR6= 0.000000 (multi-body 6th order)
138 WSCCOR= 0.000000 (back-scloc correlatkion)
139 WTURN3= 1.687220 (turns, 3rd order)
140 WTURN4= 0.662300 (turns, 4th order)
141 WTURN6= 0.000000 (turns, 6th order)
142 Reference temperature for weights calculation: 300.000000000000
143 Parameters of the SS-bond potential:
144 D0CM 3.78000000000000 AKCM 11.1621168104436 AKTH
145 8.13134337184633 AKCT 8.87055640565054
146 V1SS -0.798350076508549 V2SS 5.62541118725005 V3SS
148 EBR -5.50000000000000 SS_DEPTH -5.46701011744817
150 PDB data will be read from file a.pdb
152 Backbone and SC coordinates as read from the PDB
153 1 10 GLY -11.849 6.596 -2.403 -11.849 6.596 -2.403
154 2 9 ALA -13.418 6.572 -5.919 -12.908 6.747 -6.410
155 3 9 ALA -16.143 3.889 -6.138 -16.793 4.183 -6.397
156 4 9 ALA -13.520 1.166 -6.550 -12.785 1.239 -6.559
157 5 1 CYS -12.629 1.631 -2.805 -13.518 2.576 -2.698
158 6 9 ALA -13.467 -2.136 -2.650 -13.490 -2.860 -2.729
159 7 9 ALA -11.256 -2.842 -5.622 -11.072 -2.578 -6.320
160 8 9 ALA -8.206 -2.125 -3.496 -8.226 -1.485 -3.216
161 9 9 ALA -9.298 -4.587 -0.877 -9.634 -4.348 -0.224
162 10 9 ALA -10.565 -6.979 -3.578 -10.220 -7.012 -4.281
163 11 9 ALA -9.060 -10.399 -3.347 -9.290 -11.104 -3.486
164 12 9 ALA -5.538 -8.995 -3.201 -5.545 -8.635 -3.863
165 13 9 ALA -4.176 -7.434 -0.023 -3.823 -8.014 0.272
166 14 1 CYS -3.957 -3.989 1.621 -5.048 -3.526 1.725
167 15 9 ALA -3.473 -3.009 5.302 -3.003 -3.112 5.889
168 16 9 ALA -3.888 0.809 5.844 -4.524 1.149 5.521
169 17 9 ALA -3.394 0.685 9.610 -2.879 0.254 9.328
170 18 10 GLY -3.341 3.372 12.241 -3.341 3.372 12.241
171 nsup= 18 nstart_sup= 1
174 Geometry of the virtual chain.
175 Res d Theta Gamma Dsc Alpha Beta
176 GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
177 ALA 2 3.850 0.000 0.000 0.729 146.694 -109.363
178 ALA 3 3.830 110.272 0.000 0.759 147.957 -128.746
179 ALA 4 3.803 90.977 -78.713 0.739 105.672 -50.865
180 CYS 5 3.878 88.166 72.402 1.302 112.139 -116.564
181 ALA 6 3.862 82.642 123.024 0.729 120.951 3.720
182 ALA 7 3.771 91.361 49.351 0.769 137.392 -55.570
183 ALA 8 3.786 89.674 70.311 0.699 119.648 -87.119
184 ALA 9 3.757 91.902 53.321 0.772 145.673 -99.574
185 ALA 10 3.824 90.793 38.471 0.784 108.765 -64.768
186 ALA 11 3.744 113.246 124.426 0.754 167.686 -74.150
187 ALA 12 3.794 92.149 -50.745 0.754 133.580 -108.877
188 ALA 13 3.794 121.181 76.519 0.740 168.142 -147.575
189 CYS 14 3.823 138.722 -91.423 1.190 108.677 -76.446
190 ALA 15 3.840 130.494 158.051 0.759 141.443 -47.832
191 ALA 16 3.879 111.821 -172.250 0.790 136.439 -94.007
192 ALA 17 3.800 95.305 177.774 0.728 120.497 -127.361
193 GLY 18 3.761 132.203 178.798 0.000 0.000 0.000
214 Boundaries in phi angle sampling:
233 NZ_START= 1 NZ_END= 18
236 Geometry of the virtual chain.
237 Res d Theta Gamma Dsc Alpha Beta
238 GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
239 ALA 2 3.850 0.000 0.000 0.729 146.694 -109.363
240 ALA 3 3.830 110.272 0.000 0.759 147.957 -128.746
241 ALA 4 3.803 90.977 -78.713 0.739 105.672 -50.865
242 CYS 5 3.878 88.166 72.402 1.302 112.139 -116.564
243 ALA 6 3.862 82.642 123.024 0.729 120.951 3.720
244 ALA 7 3.771 91.361 49.351 0.769 137.392 -55.570
245 ALA 8 3.786 89.674 70.311 0.699 119.648 -87.119
246 ALA 9 3.757 91.902 53.321 0.772 145.673 -99.574
247 ALA 10 3.824 90.793 38.471 0.784 108.765 -64.768
248 ALA 11 3.744 113.246 124.426 0.754 167.686 -74.150
249 ALA 12 3.794 92.149 -50.745 0.754 133.580 -108.877
250 ALA 13 3.794 121.181 76.519 0.740 168.142 -147.575
251 CYS 14 3.823 138.722 -91.423 1.190 108.677 -76.446
252 ALA 15 3.840 130.494 158.051 0.759 141.443 -47.832
253 ALA 16 3.879 111.821 -172.250 0.790 136.439 -94.007
254 ALA 17 3.800 95.305 177.774 0.728 120.497 -127.361
255 GLY 18 3.761 132.203 178.798 0.000 0.000 0.000
257 The chain contains 2 disulfide-bridging cysteines.
259 Running with dynamic disulfide-bond formation
260 Processor 0 CG group 0 absolute rank 0 nhpb
261 0 link_start= 1 link_end 0
264 ********************************************************************************
265 Processor 0: end reading molecular data.
266 ********************************************************************************
269 Mesoscopic molecular dynamics (MD) calculation.
271 ********************************************************************************
274 ====================MD calculation start====================
275 Initial velocities randomly generated
277 0 0.33890 0.02320 0.23659 0.00000 0.00000 0.00000
278 1 -0.15077 -0.23023 -0.18811 0.00000 0.00000 0.00000
279 2 -0.14850 0.36395 0.17819 -0.06593 0.14268 0.01033
280 3 -0.01216 -0.31272 -0.40265 -0.27199 0.03880 -0.26248
281 4 0.13139 0.25689 0.25345 -0.06906 0.09806 0.19560
282 5 -0.27858 -0.01261 0.04461 -0.15425 -0.01325 -0.02214
283 6 0.09914 0.11979 0.14915 -0.11171 -0.17646 -0.10207
284 7 -0.15740 -0.32760 -0.08342 -0.15559 -0.17162 -0.27142
285 8 -0.01757 0.19689 -0.31981 -0.04208 0.07236 -0.23178
286 9 0.29843 -0.21826 0.12725 0.01235 -0.10442 -0.18484
287 10 -0.35680 0.17980 -0.11210 -0.00509 -0.02006 0.01600
288 11 0.42311 -0.07463 0.22371 0.30508 -0.03813 0.04260
289 12 -0.28440 -0.17000 -0.23671 -0.06923 -0.11283 -0.12729
290 13 0.12013 0.21611 0.14782 0.07641 0.09993 0.18719
291 14 0.15808 0.02556 -0.12952 -0.10167 -0.08786 -0.15044
292 15 -0.16543 -0.08643 0.20762 0.03124 -0.00978 0.12744
293 16 0.07008 0.14536 -0.28387 0.01006 0.26396 -0.15863
294 17 -0.12394 -0.22493 0.30015 -0.38318 -0.15223 0.30217
295 18 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
296 Calling the zero-angular momentum subroutine
297 vcm right after adjustment:
298 5.424257488318338E-018 -6.299137728369682E-018 1.504794012888313E-017
301 alpha-carbon coordinates centroid coordinates
303 GLY( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
304 ALA( 2) 3.85027 0.00000 0.00000 4.08973 0.57597 0.37779
305 ALA( 3) 5.17743 -3.59315 0.00000 5.67699 -3.69784 -0.56169
306 ALA( 4) 4.50175 -3.91184 3.72914 4.21000 -3.40822 4.18399
307 CYS( 5) 0.71590 -4.05898 2.90403 0.97457 -3.92549 1.63515
308 ALA( 6) 0.93933 -7.41535 4.80177 1.02535 -7.94644 5.29318
309 ALA( 7) 2.75671 -5.77560 7.67023 3.31749 -5.27434 7.82844
310 ALA( 8) -0.43207 -3.97536 8.63318 -0.68360 -3.58848 8.10834
311 ALA( 9) -2.36335 -7.19560 8.74835 -2.82423 -7.40238 8.16418
312 ALA( 10) 0.63437 -8.99997 10.29116 1.13596 -8.62055 10.75890
313 ALA( 11) -0.16855 -10.69479 13.53118 0.05650 -11.32099 13.88681
314 ALA( 12) -1.74585 -7.54908 14.95019 -1.14072 -7.10241 14.90335
315 ALA( 13) -5.21270 -6.43737 13.88410 -5.62232 -6.73606 14.42357
316 CYS( 14) -6.82468 -4.19410 11.24062 -6.47796 -4.54138 10.15681
317 ALA( 15) -10.38945 -4.18760 9.81345 -11.11637 -4.14078 10.02669
318 ALA( 16) -10.73908 -1.74754 6.81896 -10.18707 -1.79179 6.25526
319 ALA( 17) -14.37866 -2.58026 6.11029 -14.32832 -2.51011 6.83351
320 GLY( 18) -16.81959 -1.27490 3.56414 -16.81959 -1.27490 3.56414
322 Geometry of the virtual chain.
323 Res d Theta Gamma Dsc Alpha Beta
324 GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
325 ALA 2 3.850 0.000 0.000 0.729 146.694 -109.363
326 ALA 3 3.830 110.272 0.000 0.759 147.957 -128.746
327 ALA 4 3.803 90.977 -78.713 0.739 105.672 -50.865
328 CYS 5 3.878 88.166 72.402 1.302 112.139 -116.564
329 ALA 6 3.862 82.642 123.024 0.729 120.951 3.720
330 ALA 7 3.771 91.361 49.351 0.769 137.392 -55.570
331 ALA 8 3.786 89.674 70.311 0.699 119.648 -87.119
332 ALA 9 3.757 91.902 53.321 0.772 145.673 -99.574
333 ALA 10 3.824 90.793 38.471 0.784 108.765 -64.768
334 ALA 11 3.744 113.246 124.426 0.754 167.686 -74.150
335 ALA 12 3.794 92.149 -50.745 0.754 133.580 -108.877
336 ALA 13 3.794 121.181 76.519 0.740 168.142 -147.575
337 CYS 14 3.823 138.722 -91.423 1.190 108.677 -76.446
338 ALA 15 3.840 130.494 158.051 0.759 141.443 -47.832
339 ALA 16 3.879 111.821 -172.250 0.790 136.439 -94.007
340 ALA 17 3.800 95.305 177.774 0.728 120.497 -127.361
341 GLY 18 3.761 132.203 178.798 0.000 180.000 180.000
342 Potential energy and its components
344 Virtual-chain energies:
346 EVDW= -3.681888E+01 WEIGHT= 1.352790D+00 (SC-SC)
347 EVDW2= 2.935543E+01 WEIGHT= 1.593040D+00 (SC-p)
348 EES= -5.873651E+01 WEIGHT= 7.153400D-01 (p-p)
349 EVDWPP= -2.078573E+01 WEIGHT= 1.137100D-01 (p-p VDW)
350 ESTR= 1.126963E+01 WEIGHT= 1.000000D+00 (stretching)
351 EBE= -2.163931E+01 WEIGHT= 1.138730D+00 (bending)
352 ESC= 8.185684E+01 WEIGHT= 1.625800D-01 (SC local)
353 ETORS= 1.409747E+01 WEIGHT= 1.985990D+00 (torsional)
354 ETORSD= 3.856076E-01 WEIGHT= 1.570690D+00 (double torsional)
355 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
356 ECORR4= -3.806576E+01 WEIGHT= 4.288700D-01 (multi-body)
357 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
358 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
359 EELLO= 5.874355E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
360 ETURN3= 1.472773E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
361 ETURN4= -3.305062E+00 WEIGHT= 6.623000D-01 (turns, 4th order)
362 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
363 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
364 EDIHC= 0.000000E+00 (dihedral angle constraints)
365 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
366 UCONST= 0.000000E+00 (Constraint energy)
367 ETOT= -1.160756E+01 (total)
370 Kinetic energy 2.82436E+01
371 potential energy -1.16076E+01
372 total energy 1.66360E+01
374 maximum acceleration 1.95619E+00
376 SSBOND_FORM 129.12 300.0 5 14
377 SSBOND_BREAK 134.81 300.0 5 14
378 SSBOND_FORM 178.26 300.0 5 14
379 SSBOND_BREAK 180.34 300.0 5 14
380 SSBOND_FORM 253.52 300.0 5 14
381 SSBOND_BREAK 258.40 300.0 5 14
382 SSBOND_FORM 420.52 300.0 5 14
383 SSBOND_BREAK 421.60 300.0 5 14
384 SSBOND_FORM 425.82 300.0 5 14
385 SSBOND_BREAK 428.19 300.0 5 14
386 SSBOND_FORM 494.06 300.0 5 14
387 SSBOND_BREAK 496.25 300.0 5 14
388 SSBOND_FORM 500.25 300.0 5 14
389 SSBOND_BREAK 500.33 300.0 5 14
390 SSBOND_FORM 500.82 300.0 5 14
391 SSBOND_BREAK 501.09 300.0 5 14
392 SSBOND_FORM 520.74 300.0 5 14
393 SSBOND_BREAK 570.42 300.0 5 14
394 SSBOND_FORM 628.51 300.0 5 14
395 SSBOND_BREAK 630.04 300.0 5 14
396 SSBOND_FORM 634.06 300.0 5 14
397 SSBOND_BREAK 638.66 300.0 5 14
398 SSBOND_FORM 660.47 300.0 5 14
399 SSBOND_BREAK 661.56 300.0 5 14
400 SSBOND_FORM 671.40 300.0 5 14
401 SSBOND_BREAK 673.68 300.0 5 14
402 SSBOND_FORM 697.08 300.0 5 14
403 SSBOND_BREAK 699.21 300.0 5 14
404 SSBOND_FORM 699.76 300.0 5 14
405 SSBOND_BREAK 700.73 300.0 5 14
406 SSBOND_FORM 711.03 300.0 5 14
407 SSBOND_BREAK 713.24 300.0 5 14
408 SSBOND_FORM 714.76 300.0 5 14
409 SSBOND_BREAK 717.99 300.0 5 14
410 SSBOND_FORM 724.88 300.0 5 14
411 SSBOND_BREAK 749.39 300.0 5 14
412 SSBOND_FORM 789.73 300.0 5 14
413 SSBOND_BREAK 793.20 300.0 5 14
416 =================================== Timing ===================================
418 MD calculations setup: 1.17188E-02
419 Energy & gradient evaluation: 1.83398E+01
420 Stochastic MD setup: 0.00000E+00
421 Stochastic MD step setup: 0.00000E+00
422 MD steps: 2.30547E+01
425 ============================ End of MD calculation ===========================
426 CG processor 0 is finishing work.
427 Total wall clock time 23.0898437500000 sec