1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
5 Output file : small.out_GB
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 ### LAST MODIFIED 03/28/12 23:29 by czarek
29 ++++ Compile info ++++
31 compiled Fri Oct 5 13:10:24 2012
32 compiled by czarek@piasek3
34 OS release: 2.6.32-42-generic
35 OS version: #96-Ubuntu SMP Wed Aug 15 19:37:37 UTC 2012
38 FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
39 FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...
40 FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include
41 FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...
43 CFLAGS = -DLINUX -DPGI -c
48 object = unres.o arcos.o cartprint.o chainbuild...
49 GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...
50 GAB: BIN = ../../../bin/unres/MD/unres_ifort_si...
51 E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...
52 E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...
53 ++++ End of compile info ++++
55 Potential is GB , exponents are 6 12
57 Disulfide bridge parameters:
58 S-S bridge energy: -5.50
59 d0cm: 3.78 akcm: 15.10
60 akth: 11.00 akct: 12.00
61 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
62 ran_num 0.383569105241247
68 Time limit (min): 960.0
70 Library routine used to diagonalize matrices.
72 =========================== Parameters of the MD run ===========================
75 positions: angstrom, time: 48.9 fs
76 velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2
77 energy: kcal/mol, temperature: K
79 Number of time steps: 50000
80 Initial time step of numerical integration: 0.10000 natural units
82 Maximum acceleration threshold to reduce the time step/increase split number: 5.00000
83 Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000
84 Maximum velocity threshold to reduce velocities: 20.00000
85 Frequency of property output: 1000
86 Frequency of coordinate output: 300
87 Berendsen bath calculation
88 Temperature: 400.00000
89 Coupling constant (tau): 1.00000
90 Momenta will be reset at zero every 1000 steps
92 ============================== End of MD run setup =============================
95 Energy-term weights (unscaled):
97 WSCC= 1.000000 (SC-SC)
99 WELEC= 0.145810 (p-p electr)
100 WVDWPP= 0.145810 (p-p VDW)
101 WBOND= 1.000000 (stretching)
102 WANG= 1.956840 (bending)
103 WSCLOC= 0.170100 (SC local)
104 WTOR= 2.046980 (torsional)
105 WTORD= 1.696240 (double torsional)
106 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
107 WEL_LOC= 1.218370 (multi-body 3-rd order)
108 WCORR4= 1.846150 (multi-body 4th order)
109 WCORR5= 0.027300 (multi-body 5th order)
110 WCORR6= 0.007410 (multi-body 6th order)
111 WSCCOR= 1.000000 (back-scloc correlation)
112 WTURN3= 2.913860 (turns, 3rd order)
113 WTURN4= 0.731780 (turns, 4th order)
114 WTURN6= 0.023910 (turns, 6th order)
116 Hydrogen-bonding correlation between contact pairs of peptide groups
118 Scaling factor of 1,4 SC-p interactions: 0.400
119 General scaling factor of SC-p interactions: 1.000
121 Energy-term weights (scaled):
123 WSCC= 1.000000 (SC-SC)
124 WSCP= 2.794050 (SC-p)
125 WELEC= 0.117327 (p-p electr)
126 WVDWPP= 0.145810 (p-p VDW)
127 WBOND= 1.000000 (stretching)
128 WANG= 1.956840 (bending)
129 WSCLOC= 0.170100 (SC local)
130 WTOR= 1.647115 (torsional)
131 WTORD= 1.058472 (double torsional)
132 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
133 WEL_LOC= 0.760276 (multi-body 3-rd order)
134 WCORR4= 0.874494 (multi-body 4th order)
135 WCORR5= 0.009729 (multi-body 5th order)
136 WCORR6= 0.001982 (multi-body 6th order)
137 WSCCOR= 0.804656 (back-scloc correlatkion)
138 WTURN3= 1.818280 (turns, 3rd order)
139 WTURN4= 0.346633 (turns, 4th order)
140 WTURN6= 0.006394 (turns, 6th order)
141 Reference temperature for weights calculation: 300.000000000000
142 Parameters of the SS-bond potential:
143 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
144 11.0000000000000 AKCT 12.0000000000000
145 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
147 EBR -5.50000000000000 SS_DEPTH -6.90133843152500
148 HT 0.000000000000000E+000
168 nss= 1 ihpb,jhpb: 5 14
169 Boundaries in phi angle sampling:
188 NZ_START= 1 NZ_END= 18
190 Initial geometry will be read in.
192 Geometry of the virtual chain.
193 Res d Theta Gamma Dsc Alpha Beta
194 GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
195 ALA 2 3.800 0.000 0.000 0.743 110.000 -120.000
196 ALA 3 3.800 90.000 0.000 0.743 110.000 -120.000
197 ALA 4 3.800 90.000 180.000 0.743 110.000 -120.000
198 CYS 5 3.800 90.000 180.000 1.237 100.000 -120.000
199 ALA 6 3.800 90.000 180.000 0.743 110.000 -120.000
200 ALA 7 3.800 90.000 180.000 0.743 100.000 -120.000
201 ALA 8 3.800 90.000 180.000 0.743 110.000 -120.000
202 ALA 9 3.800 90.000 180.000 0.743 110.000 -120.000
203 ALA 10 3.800 90.000 180.000 0.743 110.000 -120.000
204 ALA 11 3.800 90.000 180.000 0.743 110.000 -120.000
205 ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000
206 ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000
207 CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000
208 ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000
209 ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000
210 ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000
211 GLY 18 3.800 90.000 180.000 0.000 0.000 0.000
213 The chain contains 2 disulfide-bridging cysteines.
216 Pre-formed links are:
218 CYS( 5) -- CYS( 14) 0.000 -5.500 0.000
220 Mesoscopic molecular dynamics (MD) calculation.
222 ********************************************************************************
225 ====================MD calculation start====================
226 Initial velocities randomly generated
228 0 -0.33453 -0.07483 -0.03206 0.00000 0.00000 0.00000
229 1 0.60801 0.09078 -0.01649 0.00000 0.00000 0.00000
230 2 -0.22717 -0.43486 0.29485 0.06489 -0.21337 0.35299
231 3 0.15327 0.53566 -0.23305 -0.24688 -0.00986 -0.12275
232 4 0.06228 -0.05375 0.06294 -0.19345 0.02670 0.20836
233 5 -0.33309 0.05139 -0.01429 -0.12351 -0.00675 -0.09273
234 6 -0.06817 -0.22870 -0.04737 0.20671 -0.13568 -0.21386
235 7 0.50143 0.23749 0.03096 -0.16319 0.01175 -0.03820
236 8 -0.13754 0.04563 0.12172 -0.02843 -0.01504 -0.10702
237 9 -0.11966 -0.06273 0.01098 -0.25787 -0.12974 -0.03183
238 10 -0.29196 -0.21182 -0.28091 -0.13032 -0.00023 -0.02943
239 11 0.17078 0.30325 0.24474 0.21168 -0.19118 0.08836
240 12 -0.02379 -0.04666 -0.03493 0.00932 -0.18572 -0.02650
241 13 0.26454 -0.06093 -0.40002 0.19547 -0.19792 0.00495
242 14 -0.36457 -0.27710 0.61404 -0.15632 0.07442 0.10234
243 15 0.14723 0.29638 -0.15981 0.45708 -0.09130 0.03430
244 16 -0.02356 0.03470 -0.42550 0.09899 -0.15554 -0.09256
245 17 0.09038 -0.11432 0.34794 -0.14072 0.01732 0.14744
246 18 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
247 Calling the zero-angular momentum subroutine
248 vcm right after adjustment:
249 1.312320360077017E-019 2.014411752718222E-017 -9.448706592554524E-018
252 alpha-carbon coordinates centroid coordinates
254 GLY( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
255 ALA( 2) 3.80000 0.00000 0.00000 3.73284 0.42654 0.60465
256 ALA( 3) 3.80000 -3.80000 0.00000 3.37346 -3.73284 -0.60465
257 ALA( 4) 7.60000 -3.80000 0.00000 7.53284 -3.37346 0.60465
258 CYS( 5) 7.60000 -7.60000 0.00000 7.01741 -7.32119 -1.05500
259 ALA( 6) 11.40000 -7.60000 0.00000 11.33284 -7.17346 0.60465
260 ALA( 7) 11.40000 -11.40000 0.00000 11.05007 -11.23253 -0.63368
261 ALA( 8) 15.20000 -11.40000 0.00000 15.13284 -10.97346 0.60465
262 ALA( 9) 15.20000 -15.20000 0.00000 14.77346 -15.13284 -0.60465
263 ALA( 10) 19.00000 -15.20000 0.00000 18.93284 -14.77346 0.60465
264 ALA( 11) 19.00000 -19.00000 0.00000 18.57346 -18.93284 -0.60465
265 ALA( 12) 22.80000 -19.00000 0.00000 22.73284 -18.57346 0.60465
266 ALA( 13) 22.80000 -22.80000 0.00000 22.45007 -22.63253 -0.63368
267 CYS( 14) 26.60000 -22.80000 0.00000 26.48819 -22.08987 1.00667
268 ALA( 15) 26.60000 -26.60000 0.00000 26.25007 -26.43253 -0.63368
269 ALA( 16) 30.40000 -26.60000 0.00000 30.33284 -26.17346 0.60465
270 ALA( 17) 30.40000 -30.40000 0.00000 29.97346 -30.33284 -0.60465
271 GLY( 18) 34.20000 -30.40000 0.00000 34.20000 -30.40000 0.00000
273 Geometry of the virtual chain.
274 Res d Theta Gamma Dsc Alpha Beta
275 GLY 1 0.000 0.000 0.000 0.000 0.000 0.000
276 ALA 2 3.800 0.000 0.000 0.743 110.000 -120.000
277 ALA 3 3.800 90.000 0.000 0.743 110.000 -120.000
278 ALA 4 3.800 90.000 180.000 0.743 110.000 -120.000
279 CYS 5 3.800 90.000 180.000 1.237 100.000 -120.000
280 ALA 6 3.800 90.000 180.000 0.743 110.000 -120.000
281 ALA 7 3.800 90.000 180.000 0.743 100.000 -120.000
282 ALA 8 3.800 90.000 180.000 0.743 110.000 -120.000
283 ALA 9 3.800 90.000 180.000 0.743 110.000 -120.000
284 ALA 10 3.800 90.000 180.000 0.743 110.000 -120.000
285 ALA 11 3.800 90.000 180.000 0.743 110.000 -120.000
286 ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000
287 ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000
288 CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000
289 ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000
290 ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000
291 ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000
292 GLY 18 3.800 90.000 180.000 0.000 180.000 180.000
293 Potential energy and its components
295 Virtual-chain energies:
297 EVDW= -1.784016E+01 WEIGHT= 1.000000D+00 (SC-SC)
298 EVDW2= 2.118779E+01 WEIGHT= 2.794050D+00 (SC-p)
299 EES= -8.122745E+00 WEIGHT= 1.173269D-01 (p-p)
300 EVDWPP= -2.540621E+01 WEIGHT= 1.458100D-01 (p-p VDW)
301 ESTR= 4.237046E-27 WEIGHT= 1.000000D+00 (stretching)
302 EBE= -1.185178E+00 WEIGHT= 1.956840D+00 (bending)
303 ESC= 1.520408E+02 WEIGHT= 1.701000D-01 (SC local)
304 ETORS= 0.000000E+00 WEIGHT= 1.647115D+00 (torsional)
305 ETORSD= -2.194244E+00 WEIGHT= 1.058472D+00 (double torsional)
306 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
307 ECORR4= 0.000000E+00 WEIGHT= 8.744941D-01 (multi-body)
308 ECORR5= 2.317900E+01 WEIGHT= 9.728750D-03 (multi-body)
309 ECORR6= 1.215220E+01 WEIGHT= 1.981519D-03 (multi-body)
310 EELLO= 3.759544E+01 WEIGHT= 7.602761D-01 (electrostatic-local)
311 ETURN3= -3.193381E+00 WEIGHT= 1.818280D+00 (turns, 3rd order)
312 ETURN4= 1.424793E+01 WEIGHT= 3.466334D-01 (turns, 4th order)
313 ETURN6= 0.000000E+00 WEIGHT= 6.393807D-03 (turns, 6th order)
314 ESCCOR= 7.779132E+00 WEIGHT= 8.046559D-01 (backbone-rotamer corr)
315 EDIHC= 0.000000E+00 (dihedral angle constraints)
316 ESS= -5.500000E+00 (disulfide-bridge intrinsic energy)
317 UCONST= 0.000000E+00 (Constraint energy)
318 ETOT= 8.664685E+01 (total)
321 Kinetic energy 4.43916E+01
322 potential energy 8.66468E+01
323 total energy 1.31038E+02
325 maximum acceleration 4.30607E+00
327 Momenta zeroed out, time 82.24
328 Momenta zeroed out, time 167.24
329 Momenta zeroed out, time 256.61
330 Momenta zeroed out, time 336.19
331 Momenta zeroed out, time 424.42
332 Momenta zeroed out, time 501.35
333 Momenta zeroed out, time 594.96
334 Momenta zeroed out, time 676.75
335 Momenta zeroed out, time 763.06
336 Momenta zeroed out, time 852.52
337 Momenta zeroed out, time 929.93
338 Momenta zeroed out, time 1011.97
339 Momenta zeroed out, time 1086.41
340 Momenta zeroed out, time 1172.78
341 Momenta zeroed out, time 1244.29
342 Momenta zeroed out, time 1327.03
343 Momenta zeroed out, time 1414.35
344 Momenta zeroed out, time 1505.75
345 Momenta zeroed out, time 1588.07
346 Momenta zeroed out, time 1682.50
347 Momenta zeroed out, time 1761.66
348 Momenta zeroed out, time 1842.58
349 Momenta zeroed out, time 1924.54
350 Momenta zeroed out, time 2006.16
351 Momenta zeroed out, time 2095.77
352 Momenta zeroed out, time 2174.07
353 Momenta zeroed out, time 2250.48
354 Momenta zeroed out, time 2327.93
355 Momenta zeroed out, time 2415.08
356 Momenta zeroed out, time 2484.46
357 Momenta zeroed out, time 2553.97
358 Momenta zeroed out, time 2639.64
359 Momenta zeroed out, time 2715.89
360 Momenta zeroed out, time 2803.24
361 Momenta zeroed out, time 2888.74
362 Momenta zeroed out, time 2967.55
363 Momenta zeroed out, time 3050.82
364 Momenta zeroed out, time 3139.25
365 Momenta zeroed out, time 3220.06
366 Momenta zeroed out, time 3310.99
367 Momenta zeroed out, time 3386.65
368 Momenta zeroed out, time 3462.21
369 Momenta zeroed out, time 3542.12
370 Momenta zeroed out, time 3625.49
371 Momenta zeroed out, time 3713.61
372 Momenta zeroed out, time 3793.08
373 Momenta zeroed out, time 3876.16
374 Momenta zeroed out, time 3955.62
375 Momenta zeroed out, time 4032.18
376 Momenta zeroed out, time 4113.16
379 =================================== Timing ===================================
381 MD calculations setup: 1.00000E-02
382 Energy & gradient evaluation: 2.00600E+01
383 Stochastic MD setup: 0.00000E+00
384 Stochastic MD step setup: 0.00000E+00
385 MD steps: 2.10900E+01
388 ============================ End of MD calculation ===========================
391 ***** Computation time: 0 hours 0 minutes 21 seconds *****