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
172 nss= 1 ihpb,jhpb: 5 14
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:
222 CYS( 5) -- CYS( 14) 0.000 -5.500 0.000
226 ********************************************************************************
227 Processor 0: end reading molecular data.
228 ********************************************************************************
231 Mesoscopic molecular dynamics (MD) calculation.
233 ********************************************************************************
236 ====================MD calculation start====================
237 Initial velocities randomly generated
239 0 0.39133 0.02679 0.27319 0.00000 0.00000 0.00000
240 1 -0.17409 -0.26585 -0.21721 0.00000 0.00000 0.00000
241 2 -0.17148 0.42025 0.20576 -0.07613 0.16475 0.01193
242 3 -0.01404 -0.36110 -0.46494 -0.31406 0.04480 -0.30309
243 4 0.15172 0.29663 0.29266 -0.07974 0.11323 0.22586
244 5 -0.32168 -0.01456 0.05151 -0.17812 -0.01530 -0.02557
245 6 0.11448 0.13832 0.17223 -0.12900 -0.20376 -0.11786
246 7 -0.18175 -0.37828 -0.09633 -0.17966 -0.19816 -0.31341
247 8 -0.02028 0.22735 -0.36928 -0.04858 0.08355 -0.26764
248 9 0.34459 -0.25203 0.14694 0.01426 -0.12058 -0.21343
249 10 -0.41200 0.20762 -0.12944 -0.00588 -0.02316 0.01848
250 11 0.48857 -0.08617 0.25832 0.35227 -0.04402 0.04919
251 12 -0.32840 -0.19630 -0.27333 -0.07994 -0.13029 -0.14699
252 13 0.13872 0.24955 0.17068 0.08823 0.11539 0.21615
253 14 0.18253 0.02951 -0.14956 -0.11740 -0.10145 -0.17371
254 15 -0.19102 -0.09980 0.23974 0.03607 -0.01130 0.14715
255 16 0.08092 0.16784 -0.32778 0.01162 0.30480 -0.18318
256 17 -0.14311 -0.25973 0.34658 -0.44245 -0.17578 0.34891
257 18 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
258 Calling the zero-angular momentum subroutine
259 vcm right after adjustment:
260 2.064717366521174E-017 -1.189837126469829E-017 5.249281440308069E-018
263 alpha-carbon coordinates centroid coordinates
265 GLY( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
266 ALA( 2) 3.80000 0.00000 0.00000 3.73284 0.42654 0.60465
267 ALA( 3) 3.80000 -3.80000 0.00000 3.37346 -3.73284 -0.60465
268 ALA( 4) 7.60000 -3.80000 0.00000 7.53284 -3.37346 0.60465
269 CYS( 5) 7.60000 -7.60000 0.00000 7.01741 -7.32119 -1.05500
270 ALA( 6) 11.40000 -7.60000 0.00000 11.33284 -7.17346 0.60465
271 ALA( 7) 11.40000 -11.40000 0.00000 11.05007 -11.23253 -0.63368
272 ALA( 8) 15.20000 -11.40000 0.00000 15.13284 -10.97346 0.60465
273 ALA( 9) 15.20000 -15.20000 0.00000 14.77346 -15.13284 -0.60465
274 ALA( 10) 19.00000 -15.20000 0.00000 18.93284 -14.77346 0.60465
275 ALA( 11) 19.00000 -19.00000 0.00000 18.57346 -18.93284 -0.60465
276 ALA( 12) 22.80000 -19.00000 0.00000 22.73284 -18.57346 0.60465
277 ALA( 13) 22.80000 -22.80000 0.00000 22.45007 -22.63253 -0.63368
278 CYS( 14) 26.60000 -22.80000 0.00000 26.48819 -22.08987 1.00667
279 ALA( 15) 26.60000 -26.60000 0.00000 26.25007 -26.43253 -0.63368
280 ALA( 16) 30.40000 -26.60000 0.00000 30.33284 -26.17346 0.60465
281 ALA( 17) 30.40000 -30.40000 0.00000 29.97346 -30.33284 -0.60465
282 GLY( 18) 34.20000 -30.40000 0.00000 34.20000 -30.40000 0.00000
284 Geometry of the virtual chain.
285 Res d Theta Gamma Dsc Alpha Beta
286 GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
287 ALA 2 3.800 0.000 0.000 0.743 110.000 -120.000
288 ALA 3 3.800 90.000 0.000 0.743 110.000 -120.000
289 ALA 4 3.800 90.000 180.000 0.743 110.000 -120.000
290 CYS 5 3.800 90.000 180.000 1.237 100.000 -120.000
291 ALA 6 3.800 90.000 180.000 0.743 110.000 -120.000
292 ALA 7 3.800 90.000 180.000 0.743 100.000 -120.000
293 ALA 8 3.800 90.000 180.000 0.743 110.000 -120.000
294 ALA 9 3.800 90.000 180.000 0.743 110.000 -120.000
295 ALA 10 3.800 90.000 180.000 0.743 110.000 -120.000
296 ALA 11 3.800 90.000 180.000 0.743 110.000 -120.000
297 ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000
298 ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000
299 CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000
300 ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000
301 ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000
302 ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000
303 GLY 18 3.800 90.000 180.000 0.000 180.000 180.000
304 Potential energy and its components
306 Virtual-chain energies:
308 EVDW= -1.784016E+01 WEIGHT= 1.000000D+00 (SC-SC)
309 EVDW2= 2.118779E+01 WEIGHT= 2.794050D+00 (SC-p)
310 EES= -8.122745E+00 WEIGHT= 1.173269D-01 (p-p)
311 EVDWPP= -2.540621E+01 WEIGHT= 1.458100D-01 (p-p VDW)
312 ESTR= 4.237046E-27 WEIGHT= 1.000000D+00 (stretching)
313 EBE= -1.185178E+00 WEIGHT= 1.956840D+00 (bending)
314 ESC= 1.520408E+02 WEIGHT= 1.701000D-01 (SC local)
315 ETORS= 0.000000E+00 WEIGHT= 1.647115D+00 (torsional)
316 ETORSD= -2.194244E+00 WEIGHT= 1.058472D+00 (double torsional)
317 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
318 ECORR4= -5.324225E+00 WEIGHT= 8.744941D-01 (multi-body)
319 ECORR5= 2.317900E+01 WEIGHT= 9.728750D-03 (multi-body)
320 ECORR6= 1.215220E+01 WEIGHT= 1.981519D-03 (multi-body)
321 EELLO= 3.759544E+01 WEIGHT= 7.602761D-01 (electrostatic-local)
322 ETURN3= -3.193381E+00 WEIGHT= 1.818280D+00 (turns, 3rd order)
323 ETURN4= 1.424793E+01 WEIGHT= 3.466334D-01 (turns, 4th order)
324 ETURN6= 0.000000E+00 WEIGHT= 6.393807D-03 (turns, 6th order)
325 ESCCOR= 7.779132E+00 WEIGHT= 8.046559D-01 (backbone-rotamer corr)
326 EDIHC= 0.000000E+00 (dihedral angle constraints)
327 ESS= -5.500000E+00 (disulfide-bridge intrinsic energy)
328 UCONST= 0.000000E+00 (Constraint energy)
329 ETOT= 8.199085E+01 (total)
332 Kinetic energy 3.88148E+01
333 potential energy 8.19908E+01
334 total energy 1.20806E+02
336 maximum acceleration 4.30399E+00
338 Momenta zeroed out, time 91.45
339 Momenta zeroed out, time 184.03
340 Momenta zeroed out, time 272.29
341 Momenta zeroed out, time 352.66
342 Momenta zeroed out, time 433.97
343 Momenta zeroed out, time 511.45
344 Momenta zeroed out, time 580.99
345 Momenta zeroed out, time 659.41
346 Momenta zeroed out, time 747.14
347 Momenta zeroed out, time 828.82
348 Momenta zeroed out, time 908.82
349 Momenta zeroed out, time 999.77
350 Momenta zeroed out, time 1088.79
351 Momenta zeroed out, time 1164.32
352 Momenta zeroed out, time 1251.79
353 Momenta zeroed out, time 1325.55
354 Momenta zeroed out, time 1406.48
355 Momenta zeroed out, time 1488.30
356 Momenta zeroed out, time 1565.08
357 Momenta zeroed out, time 1643.57
358 Momenta zeroed out, time 1718.65
359 Momenta zeroed out, time 1800.99
360 Momenta zeroed out, time 1884.00
361 Momenta zeroed out, time 1971.64
362 Momenta zeroed out, time 2048.36
363 Momenta zeroed out, time 2124.95
364 Momenta zeroed out, time 2217.16
365 Momenta zeroed out, time 2300.04
366 Momenta zeroed out, time 2384.50
367 Momenta zeroed out, time 2466.73
368 Momenta zeroed out, time 2552.30
369 Momenta zeroed out, time 2639.36
370 Momenta zeroed out, time 2726.62
371 Momenta zeroed out, time 2816.04
372 Momenta zeroed out, time 2898.68
373 Momenta zeroed out, time 2991.02
374 Momenta zeroed out, time 3076.75
375 Momenta zeroed out, time 3153.54
376 Momenta zeroed out, time 3233.35
377 Momenta zeroed out, time 3304.91
378 Momenta zeroed out, time 3391.89
379 Momenta zeroed out, time 3482.06
380 Momenta zeroed out, time 3572.05
381 Momenta zeroed out, time 3647.43
382 Momenta zeroed out, time 3735.02
383 Momenta zeroed out, time 3818.88
384 Momenta zeroed out, time 3905.50
385 Momenta zeroed out, time 3989.66
386 Momenta zeroed out, time 4071.09
387 Momenta zeroed out, time 4142.60
390 =================================== Timing ===================================
392 MD calculations setup: 4.68750E-02
393 Energy & gradient evaluation: 2.06914E+01
394 Stochastic MD setup: 0.00000E+00
395 Stochastic MD step setup: 0.00000E+00
396 MD steps: 2.45156E+01
399 ============================ End of MD calculation ===========================
400 CG processor 0 is finishing work.
401 Total wall clock time 24.9843750000000 sec