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 Wed Nov 7 12:05:42 2012
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: 50000
84 Initial time step of numerical integration: 0.10000 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: 1000
90 Frequency of coordinate output: 300
91 Berendsen bath calculation
92 Temperature: 400.00000
93 Coupling constant (tau): 1.00000
94 Momenta will be reset at zero every 1000 steps
96 ============================== End of MD run setup =============================
99 Energy-term weights (unscaled):
101 WSCC= 1.000000 (SC-SC)
102 WSCP= 2.794050 (SC-p)
103 WELEC= 0.145810 (p-p electr)
104 WVDWPP= 0.145810 (p-p VDW)
105 WBOND= 1.000000 (stretching)
106 WANG= 1.956840 (bending)
107 WSCLOC= 0.170100 (SC local)
108 WTOR= 2.046980 (torsional)
109 WTORD= 1.696240 (double torsional)
110 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
111 WEL_LOC= 1.218370 (multi-body 3-rd order)
112 WCORR4= 1.846150 (multi-body 4th order)
113 WCORR5= 0.027300 (multi-body 5th order)
114 WCORR6= 0.007410 (multi-body 6th order)
115 WSCCOR= 1.000000 (back-scloc correlation)
116 WTURN3= 2.913860 (turns, 3rd order)
117 WTURN4= 0.731780 (turns, 4th order)
118 WTURN6= 0.023910 (turns, 6th order)
120 Hydrogen-bonding correlation between contact pairs of peptide groups
122 Scaling factor of 1,4 SC-p interactions: 0.400
123 General scaling factor of SC-p interactions: 1.000
125 Energy-term weights (scaled):
127 WSCC= 1.000000 (SC-SC)
128 WSCP= 2.794050 (SC-p)
129 WELEC= 0.117327 (p-p electr)
130 WVDWPP= 0.145810 (p-p VDW)
131 WBOND= 1.000000 (stretching)
132 WANG= 1.956840 (bending)
133 WSCLOC= 0.170100 (SC local)
134 WTOR= 1.647115 (torsional)
135 WTORD= 1.058472 (double torsional)
136 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
137 WEL_LOC= 0.760276 (multi-body 3-rd order)
138 WCORR4= 0.874494 (multi-body 4th order)
139 WCORR5= 0.009729 (multi-body 5th order)
140 WCORR6= 0.001982 (multi-body 6th order)
141 WSCCOR= 0.804656 (back-scloc correlatkion)
142 WTURN3= 1.818280 (turns, 3rd order)
143 WTURN4= 0.346633 (turns, 4th order)
144 WTURN6= 0.006394 (turns, 6th order)
145 Reference temperature for weights calculation: 300.000000000000
146 Parameters of the SS-bond potential:
147 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
148 11.0000000000000 AKCT 12.0000000000000
149 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
151 EBR -5.50000000000000 SS_DEPTH -6.90133843152500
152 HT 0.000000000000000E+000
173 Boundaries in phi angle sampling:
192 NZ_START= 1 NZ_END= 18
194 Initial geometry will be read in.
196 Geometry of the virtual chain.
197 Res d Theta Gamma Dsc Alpha Beta
198 GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
199 ALA 2 3.800 0.000 0.000 0.743 110.000 -120.000
200 ALA 3 3.800 90.000 0.000 0.743 110.000 -120.000
201 ALA 4 3.800 90.000 180.000 0.743 110.000 -120.000
202 CYS 5 3.800 90.000 180.000 1.237 100.000 -120.000
203 ALA 6 3.800 90.000 180.000 0.743 110.000 -120.000
204 ALA 7 3.800 90.000 180.000 0.743 100.000 -120.000
205 ALA 8 3.800 90.000 180.000 0.743 110.000 -120.000
206 ALA 9 3.800 90.000 180.000 0.743 110.000 -120.000
207 ALA 10 3.800 90.000 180.000 0.743 110.000 -120.000
208 ALA 11 3.800 90.000 180.000 0.743 110.000 -120.000
209 ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000
210 ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000
211 CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000
212 ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000
213 ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000
214 ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000
215 GLY 18 3.800 90.000 180.000 0.000 0.000 0.000
217 The chain contains 2 disulfide-bridging cysteines.
220 Pre-formed links are:
225 ********************************************************************************
226 Processor 0: end reading molecular data.
227 ********************************************************************************
230 Mesoscopic molecular dynamics (MD) calculation.
232 ********************************************************************************
235 ====================MD calculation start====================
236 Initial velocities randomly generated
238 0 0.39133 0.02679 0.27319 0.00000 0.00000 0.00000
239 1 -0.17409 -0.26585 -0.21721 0.00000 0.00000 0.00000
240 2 -0.17148 0.42025 0.20576 -0.07613 0.16475 0.01193
241 3 -0.01404 -0.36110 -0.46494 -0.31406 0.04480 -0.30309
242 4 0.15172 0.29663 0.29266 -0.07974 0.11323 0.22586
243 5 -0.32168 -0.01456 0.05151 -0.17812 -0.01530 -0.02557
244 6 0.11448 0.13832 0.17223 -0.12900 -0.20376 -0.11786
245 7 -0.18175 -0.37828 -0.09633 -0.17966 -0.19816 -0.31341
246 8 -0.02028 0.22735 -0.36928 -0.04858 0.08355 -0.26764
247 9 0.34459 -0.25203 0.14694 0.01426 -0.12058 -0.21343
248 10 -0.41200 0.20762 -0.12944 -0.00588 -0.02316 0.01848
249 11 0.48857 -0.08617 0.25832 0.35227 -0.04402 0.04919
250 12 -0.32840 -0.19630 -0.27333 -0.07994 -0.13029 -0.14699
251 13 0.13872 0.24955 0.17068 0.08823 0.11539 0.21615
252 14 0.18253 0.02951 -0.14956 -0.11740 -0.10145 -0.17371
253 15 -0.19102 -0.09980 0.23974 0.03607 -0.01130 0.14715
254 16 0.08092 0.16784 -0.32778 0.01162 0.30480 -0.18318
255 17 -0.14311 -0.25973 0.34658 -0.44245 -0.17578 0.34891
256 18 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
257 Calling the zero-angular momentum subroutine
258 vcm right after adjustment:
259 2.064717366521174E-017 -1.189837126469829E-017 5.249281440308069E-018
262 alpha-carbon coordinates centroid coordinates
264 GLY( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
265 ALA( 2) 3.80000 0.00000 0.00000 3.73284 0.42654 0.60465
266 ALA( 3) 3.80000 -3.80000 0.00000 3.37346 -3.73284 -0.60465
267 ALA( 4) 7.60000 -3.80000 0.00000 7.53284 -3.37346 0.60465
268 CYS( 5) 7.60000 -7.60000 0.00000 7.01741 -7.32119 -1.05500
269 ALA( 6) 11.40000 -7.60000 0.00000 11.33284 -7.17346 0.60465
270 ALA( 7) 11.40000 -11.40000 0.00000 11.05007 -11.23253 -0.63368
271 ALA( 8) 15.20000 -11.40000 0.00000 15.13284 -10.97346 0.60465
272 ALA( 9) 15.20000 -15.20000 0.00000 14.77346 -15.13284 -0.60465
273 ALA( 10) 19.00000 -15.20000 0.00000 18.93284 -14.77346 0.60465
274 ALA( 11) 19.00000 -19.00000 0.00000 18.57346 -18.93284 -0.60465
275 ALA( 12) 22.80000 -19.00000 0.00000 22.73284 -18.57346 0.60465
276 ALA( 13) 22.80000 -22.80000 0.00000 22.45007 -22.63253 -0.63368
277 CYS( 14) 26.60000 -22.80000 0.00000 26.48819 -22.08987 1.00667
278 ALA( 15) 26.60000 -26.60000 0.00000 26.25007 -26.43253 -0.63368
279 ALA( 16) 30.40000 -26.60000 0.00000 30.33284 -26.17346 0.60465
280 ALA( 17) 30.40000 -30.40000 0.00000 29.97346 -30.33284 -0.60465
281 GLY( 18) 34.20000 -30.40000 0.00000 34.20000 -30.40000 0.00000
283 Geometry of the virtual chain.
284 Res d Theta Gamma Dsc Alpha Beta
285 GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
286 ALA 2 3.800 0.000 0.000 0.743 110.000 -120.000
287 ALA 3 3.800 90.000 0.000 0.743 110.000 -120.000
288 ALA 4 3.800 90.000 180.000 0.743 110.000 -120.000
289 CYS 5 3.800 90.000 180.000 1.237 100.000 -120.000
290 ALA 6 3.800 90.000 180.000 0.743 110.000 -120.000
291 ALA 7 3.800 90.000 180.000 0.743 100.000 -120.000
292 ALA 8 3.800 90.000 180.000 0.743 110.000 -120.000
293 ALA 9 3.800 90.000 180.000 0.743 110.000 -120.000
294 ALA 10 3.800 90.000 180.000 0.743 110.000 -120.000
295 ALA 11 3.800 90.000 180.000 0.743 110.000 -120.000
296 ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000
297 ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000
298 CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000
299 ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000
300 ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000
301 ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000
302 GLY 18 3.800 90.000 180.000 0.000 180.000 180.000
303 Potential energy and its components
305 Virtual-chain energies:
307 EVDW= -1.784028E+01 WEIGHT= 1.000000D+00 (SC-SC)
308 EVDW2= 2.118779E+01 WEIGHT= 2.794050D+00 (SC-p)
309 EES= -8.122745E+00 WEIGHT= 1.173269D-01 (p-p)
310 EVDWPP= -2.540621E+01 WEIGHT= 1.458100D-01 (p-p VDW)
311 ESTR= 4.237046E-27 WEIGHT= 1.000000D+00 (stretching)
312 EBE= -1.185178E+00 WEIGHT= 1.956840D+00 (bending)
313 ESC= 1.520408E+02 WEIGHT= 1.701000D-01 (SC local)
314 ETORS= 0.000000E+00 WEIGHT= 1.647115D+00 (torsional)
315 ETORSD= -2.194244E+00 WEIGHT= 1.058472D+00 (double torsional)
316 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
317 ECORR4= -5.324225E+00 WEIGHT= 8.744941D-01 (multi-body)
318 ECORR5= 2.317900E+01 WEIGHT= 9.728750D-03 (multi-body)
319 ECORR6= 1.215220E+01 WEIGHT= 1.981519D-03 (multi-body)
320 EELLO= 3.759544E+01 WEIGHT= 7.602761D-01 (electrostatic-local)
321 ETURN3= -3.193381E+00 WEIGHT= 1.818280D+00 (turns, 3rd order)
322 ETURN4= 1.424793E+01 WEIGHT= 3.466334D-01 (turns, 4th order)
323 ETURN6= 0.000000E+00 WEIGHT= 6.393807D-03 (turns, 6th order)
324 ESCCOR= 7.779132E+00 WEIGHT= 8.046559D-01 (backbone-rotamer corr)
325 EDIHC= 0.000000E+00 (dihedral angle constraints)
326 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
327 UCONST= 0.000000E+00 (Constraint energy)
328 ETOT= 8.749073E+01 (total)
331 Kinetic energy 3.88148E+01
332 potential energy 8.74907E+01
333 total energy 1.26306E+02
335 maximum acceleration 4.30399E+00
337 Momenta zeroed out, time 89.72
338 Momenta zeroed out, time 184.80
339 Momenta zeroed out, time 255.62
340 Momenta zeroed out, time 334.60
341 Momenta zeroed out, time 415.00
342 Momenta zeroed out, time 498.96
343 Momenta zeroed out, time 586.14
344 Momenta zeroed out, time 675.88
345 Momenta zeroed out, time 766.19
346 Momenta zeroed out, time 847.02
347 Momenta zeroed out, time 934.67
348 Momenta zeroed out, time 1018.19
349 Momenta zeroed out, time 1112.72
350 Momenta zeroed out, time 1197.49
351 Momenta zeroed out, time 1281.88
352 Momenta zeroed out, time 1363.69
353 Momenta zeroed out, time 1440.30
354 Momenta zeroed out, time 1524.49
355 Momenta zeroed out, time 1613.51
356 Momenta zeroed out, time 1693.76
357 Momenta zeroed out, time 1784.30
358 Momenta zeroed out, time 1866.61
359 Momenta zeroed out, time 1957.29
360 Momenta zeroed out, time 2045.18
361 Momenta zeroed out, time 2132.51
362 Momenta zeroed out, time 2222.74
363 Momenta zeroed out, time 2308.03
364 Momenta zeroed out, time 2386.51
365 Momenta zeroed out, time 2465.39
366 Momenta zeroed out, time 2545.75
367 Momenta zeroed out, time 2626.03
368 Momenta zeroed out, time 2712.22
369 Momenta zeroed out, time 2790.06
370 Momenta zeroed out, time 2856.14
371 Momenta zeroed out, time 2935.37
372 Momenta zeroed out, time 3026.25
373 Momenta zeroed out, time 3115.49
374 Momenta zeroed out, time 3197.76
375 Momenta zeroed out, time 3280.83
376 Momenta zeroed out, time 3361.57
377 Momenta zeroed out, time 3435.50
378 Momenta zeroed out, time 3501.99
379 Momenta zeroed out, time 3588.70
380 Momenta zeroed out, time 3675.90
381 Momenta zeroed out, time 3760.47
382 Momenta zeroed out, time 3843.93
383 Momenta zeroed out, time 3930.62
384 Momenta zeroed out, time 4021.79
385 Momenta zeroed out, time 4102.92
386 Momenta zeroed out, time 4199.64
389 =================================== Timing ===================================
391 MD calculations setup: 9.37500E-02
392 Energy & gradient evaluation: 2.02773E+01
393 Stochastic MD setup: 0.00000E+00
394 Stochastic MD step setup: 0.00000E+00
395 MD steps: 2.93281E+01
398 ============================ End of MD calculation ===========================
399 CG processor 0 is finishing work.
400 Total wall clock time 29.8750000000000 sec