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 01:43:03 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: 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
172 nss= 1 ihpb,jhpb: 5 14
173 Boundaries in phi angle sampling:
192 NZ_START= 1 NZ_END= 18
194 Processor 0 CG group 0 absolute rank 0 nhpb
195 1 link_start= 1 link_end 1
196 Initial geometry will be read in.
198 Geometry of the virtual chain.
199 Res d Theta Gamma Dsc Alpha Beta
200 GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
201 ALA 2 3.800 0.000 0.000 0.743 110.000 -120.000
202 ALA 3 3.800 90.000 0.000 0.743 110.000 -120.000
203 ALA 4 3.800 90.000 180.000 0.743 110.000 -120.000
204 CYS 5 3.800 90.000 180.000 1.237 100.000 -120.000
205 ALA 6 3.800 90.000 180.000 0.743 110.000 -120.000
206 ALA 7 3.800 90.000 180.000 0.743 100.000 -120.000
207 ALA 8 3.800 90.000 180.000 0.743 110.000 -120.000
208 ALA 9 3.800 90.000 180.000 0.743 110.000 -120.000
209 ALA 10 3.800 90.000 180.000 0.743 110.000 -120.000
210 ALA 11 3.800 90.000 180.000 0.743 110.000 -120.000
211 ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000
212 ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000
213 CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000
214 ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000
215 ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000
216 ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000
217 GLY 18 3.800 90.000 180.000 0.000 0.000 0.000
219 The chain contains 2 disulfide-bridging cysteines.
222 Pre-formed links are:
224 CYS( 5) -- CYS( 14) 0.000 -5.500 0.000
228 ********************************************************************************
229 Processor 0: end reading molecular data.
230 ********************************************************************************
233 Mesoscopic molecular dynamics (MD) calculation.
235 ********************************************************************************
238 ====================MD calculation start====================
239 Initial velocities randomly generated
241 0 0.39133 0.02679 0.27319 0.00000 0.00000 0.00000
242 1 -0.17409 -0.26585 -0.21721 0.00000 0.00000 0.00000
243 2 -0.17148 0.42025 0.20576 -0.07613 0.16475 0.01193
244 3 -0.01404 -0.36110 -0.46494 -0.31406 0.04480 -0.30309
245 4 0.15172 0.29663 0.29266 -0.07974 0.11323 0.22586
246 5 -0.32168 -0.01456 0.05151 -0.17812 -0.01530 -0.02557
247 6 0.11448 0.13832 0.17223 -0.12900 -0.20376 -0.11786
248 7 -0.18175 -0.37828 -0.09633 -0.17966 -0.19816 -0.31341
249 8 -0.02028 0.22735 -0.36928 -0.04858 0.08355 -0.26764
250 9 0.34459 -0.25203 0.14694 0.01426 -0.12058 -0.21343
251 10 -0.41200 0.20762 -0.12944 -0.00588 -0.02316 0.01848
252 11 0.48857 -0.08617 0.25832 0.35227 -0.04402 0.04919
253 12 -0.32840 -0.19630 -0.27333 -0.07994 -0.13029 -0.14699
254 13 0.13872 0.24955 0.17068 0.08823 0.11539 0.21615
255 14 0.18253 0.02951 -0.14956 -0.11740 -0.10145 -0.17371
256 15 -0.19102 -0.09980 0.23974 0.03607 -0.01130 0.14715
257 16 0.08092 0.16784 -0.32778 0.01162 0.30480 -0.18318
258 17 -0.14311 -0.25973 0.34658 -0.44245 -0.17578 0.34891
259 18 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
260 Calling the zero-angular momentum subroutine
261 vcm right after adjustment:
262 2.064717366521174E-017 -1.189837126469829E-017 5.249281440308069E-018
265 alpha-carbon coordinates centroid coordinates
267 GLY( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
268 ALA( 2) 3.80000 0.00000 0.00000 3.73284 0.42654 0.60465
269 ALA( 3) 3.80000 -3.80000 0.00000 3.37346 -3.73284 -0.60465
270 ALA( 4) 7.60000 -3.80000 0.00000 7.53284 -3.37346 0.60465
271 CYS( 5) 7.60000 -7.60000 0.00000 7.01741 -7.32119 -1.05500
272 ALA( 6) 11.40000 -7.60000 0.00000 11.33284 -7.17346 0.60465
273 ALA( 7) 11.40000 -11.40000 0.00000 11.05007 -11.23253 -0.63368
274 ALA( 8) 15.20000 -11.40000 0.00000 15.13284 -10.97346 0.60465
275 ALA( 9) 15.20000 -15.20000 0.00000 14.77346 -15.13284 -0.60465
276 ALA( 10) 19.00000 -15.20000 0.00000 18.93284 -14.77346 0.60465
277 ALA( 11) 19.00000 -19.00000 0.00000 18.57346 -18.93284 -0.60465
278 ALA( 12) 22.80000 -19.00000 0.00000 22.73284 -18.57346 0.60465
279 ALA( 13) 22.80000 -22.80000 0.00000 22.45007 -22.63253 -0.63368
280 CYS( 14) 26.60000 -22.80000 0.00000 26.48819 -22.08987 1.00667
281 ALA( 15) 26.60000 -26.60000 0.00000 26.25007 -26.43253 -0.63368
282 ALA( 16) 30.40000 -26.60000 0.00000 30.33284 -26.17346 0.60465
283 ALA( 17) 30.40000 -30.40000 0.00000 29.97346 -30.33284 -0.60465
284 GLY( 18) 34.20000 -30.40000 0.00000 34.20000 -30.40000 0.00000
286 Geometry of the virtual chain.
287 Res d Theta Gamma Dsc Alpha Beta
288 GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
289 ALA 2 3.800 0.000 0.000 0.743 110.000 -120.000
290 ALA 3 3.800 90.000 0.000 0.743 110.000 -120.000
291 ALA 4 3.800 90.000 180.000 0.743 110.000 -120.000
292 CYS 5 3.800 90.000 180.000 1.237 100.000 -120.000
293 ALA 6 3.800 90.000 180.000 0.743 110.000 -120.000
294 ALA 7 3.800 90.000 180.000 0.743 100.000 -120.000
295 ALA 8 3.800 90.000 180.000 0.743 110.000 -120.000
296 ALA 9 3.800 90.000 180.000 0.743 110.000 -120.000
297 ALA 10 3.800 90.000 180.000 0.743 110.000 -120.000
298 ALA 11 3.800 90.000 180.000 0.743 110.000 -120.000
299 ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000
300 ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000
301 CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000
302 ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000
303 ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000
304 ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000
305 GLY 18 3.800 90.000 180.000 0.000 180.000 180.000
306 Potential energy and its components
308 Virtual-chain energies:
310 EVDW= -1.784016E+01 WEIGHT= 1.000000E+00 (SC-SC)
311 EVDW2= 2.118779E+01 WEIGHT= 2.794050E+00 (SC-p)
312 EES= -8.122745E+00 WEIGHT= 1.173269E-01 (p-p)
313 EVDWPP= -2.540621E+01 WEIGHT= 1.458100E-01 (p-p VDW)
314 ESTR= 4.237046E-27 WEIGHT= 1.000000E+00 (stretching)
315 EBE= -1.185178E+00 WEIGHT= 1.956840E+00 (bending)
316 ESC= 1.520408E+02 WEIGHT= 1.701000E-01 (SC local)
317 ETORS= 0.000000E+00 WEIGHT= 1.647115E+00 (torsional)
318 ETORSD= -2.194244E+00 WEIGHT= 1.058472E+00 (double torsional)
319 EHPB= 7.073396E+03 WEIGHT= 1.000000E+00 (SS bridges & dist. cnstr.)
320 ECORR4= -5.324225E+00 WEIGHT= 8.744941E-01 (multi-body)
321 ECORR5= 2.317900E+01 WEIGHT= 9.728750E-03 (multi-body)
322 ECORR6= 1.215220E+01 WEIGHT= 1.981519E-03 (multi-body)
323 EELLO= 3.759544E+01 WEIGHT= 7.602761E-01 (electrostatic-local)
324 ETURN3= -3.193381E+00 WEIGHT= 1.818280E+00 (turns, 3rd order)
325 ETURN4= 1.424793E+01 WEIGHT= 3.466334E-01 (turns, 4th order)
326 ETURN6= 0.000000E+00 WEIGHT= 6.393807E-03 (turns, 6th order)
327 ESCCOR= 7.779132E+00 WEIGHT= 8.046559E-01 (backbone-rotamer corr)
328 EDIHC= 0.000000E+00 (dihedral angle constraints)
329 ESS= -5.500000E+00 (disulfide-bridge intrinsic energy)
330 UCONST= 0.000000E+00 (Constraint energy)
331 ETOT= 7.160887E+03 (total)
334 Kinetic energy 3.88148E+01
335 potential energy 7.16089E+03
336 total energy 7.19970E+03
338 maximum acceleration 8.95527E+00
340 Momenta zeroed out, time 74.69
341 Momenta zeroed out, time 155.43
342 Momenta zeroed out, time 241.84
343 Momenta zeroed out, time 328.70
344 Momenta zeroed out, time 421.23
345 Momenta zeroed out, time 511.98
346 Momenta zeroed out, time 602.19
347 Momenta zeroed out, time 692.58
348 Momenta zeroed out, time 772.45
349 Momenta zeroed out, time 858.53
350 Momenta zeroed out, time 950.14
351 Momenta zeroed out, time 1046.56
352 Momenta zeroed out, time 1135.95
353 Momenta zeroed out, time 1229.34
354 Momenta zeroed out, time 1313.26
355 Momenta zeroed out, time 1405.83
356 Momenta zeroed out, time 1497.00
357 Momenta zeroed out, time 1578.41
358 Momenta zeroed out, time 1666.29
359 Momenta zeroed out, time 1745.56
360 Momenta zeroed out, time 1831.56
361 Momenta zeroed out, time 1919.91
362 Momenta zeroed out, time 2004.48
363 Momenta zeroed out, time 2088.04
364 Momenta zeroed out, time 2176.84
365 Momenta zeroed out, time 2264.56
366 Momenta zeroed out, time 2358.16
367 Momenta zeroed out, time 2444.18
368 Momenta zeroed out, time 2536.32
369 Momenta zeroed out, time 2626.16
370 Momenta zeroed out, time 2724.47
371 Momenta zeroed out, time 2809.21
372 Momenta zeroed out, time 2898.49
373 Momenta zeroed out, time 2997.11
374 Momenta zeroed out, time 3091.11
375 Momenta zeroed out, time 3179.33
376 Momenta zeroed out, time 3273.79
377 Momenta zeroed out, time 3364.47
378 Momenta zeroed out, time 3447.21
379 Momenta zeroed out, time 3536.79
380 Momenta zeroed out, time 3612.39
381 Momenta zeroed out, time 3696.49
382 Momenta zeroed out, time 3791.89
383 Momenta zeroed out, time 3881.13
384 Momenta zeroed out, time 3975.76
385 Momenta zeroed out, time 4058.45
386 Momenta zeroed out, time 4141.61
387 Momenta zeroed out, time 4236.95
388 Momenta zeroed out, time 4322.86
389 Momenta zeroed out, time 4404.87
392 =================================== Timing ===================================
394 MD calculations setup: 7.81250E-03
395 Energy & gradient evaluation: 2.36836E+01
396 Stochastic MD setup: 0.00000E+00
397 Stochastic MD step setup: 0.00000E+00
398 MD steps: 2.49102E+01
401 ============================ End of MD calculation ===========================
402 CG processor 0 is finishing work.
403 Total wall clock time 24.9453125000000 sec