1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1L2Y_MD.inp
5 Output file : 1L2Y_MD.out_GB000
7 Sidechain potential file :
8 /users/aks255/newUNRES/unres/PARAM/scinter_GB.parm
9 SCp potential file : /users/aks255/newUNRES/unres/PARAM/scp.parm
10 Electrostatic potential file :
11 /users/aks255/newUNRES/unres/PARAM/electr_631Gdp.parm
12 Cumulant coefficient file :
13 /users/aks255/newUNRES/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3
14 Torsional parameter file :
15 /users/aks255/newUNRES/unres/PARAM/torsion_631Gdp.parm
16 Double torsional parameter file :
17 /users/aks255/newUNRES/unres/PARAM/torsion_double_631Gdp.parm
18 SCCOR parameter file : /users/aks255/newUNRES/unres/PARAM/sccor_pdb_shelly.dat
19 Bond & inertia constant file :
20 /users/aks255/newUNRES/unres/PARAM/bond_AM1.parm
21 Bending parameter file :
22 /users/aks255/newUNRES/unres/PARAM/theta_abinitio.parm
23 Rotamer parameter file :
24 /users/aks255/newUNRES/unres/PARAM/rotamers_AM1_aura.10022007.parm
26 /users/aks255/newUNRES/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 Thu Jul 5 05:49:13 2012
35 compiled by jal47@matrix.chem.cornell.edu
37 OS release: 2.6.34.9-69.fc13.x86_64
38 OS version: #1 SMP Tue May 3 09:23:03 UTC 2011
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 ++++
56 Start reading THETA_PDB
59 Potential is GB , exponents are 6 12
61 Disulfide bridge parameters:
62 S-S bridge energy: -5.50
63 d0cm: 3.78 akcm: 15.10
64 akth: 11.00 akct: 12.00
65 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
66 MPI: node= 0 iseed(4)= 0 0 -46
68 ran_num 6.422640197456531E-013
74 Time limit (min): 960.0
76 Library routine used to diagonalize matrices.
78 =========================== Parameters of the MD run ===========================
81 positions: angstrom, time: 48.9 fs
82 velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2
83 energy: kcal/mol, temperature: K
85 Number of time steps: 1000000
86 Initial time step of numerical integration: 0.20000 natural units
88 A-MTS algorithm used; initial time step for fast-varying short-range forces split into 1 steps.
89 Short-range force cutoff 2.00 lambda 0.30
90 Maximum acceleration threshold to reduce the time step/increase split number: 10.00000
91 Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000
92 Maximum velocity threshold to reduce velocities: 20.00000
93 Frequency of property output: 10000
94 Frequency of coordinate output: 10000
96 Langevin dynamics calculation with direct integration of Langevin equations
98 Temperature: 300.00000
99 Viscosity of the solvent: 0.89040
100 Radius of solvent molecule: 1.40000
101 Scaling factor of the friction forces: 0.02000
102 Eta of the solvent in natural units: 49.27846
104 Radii of site types and friction coefficients and std's of stochastic forces of fully exposed sites
106 p 2.50 3.84372 4.78549
107 CYS 5.00 6.30764 6.13033
108 MET 6.20 7.49033 6.68037
109 PHE 6.80 8.08167 6.93906
110 ILE 6.20 7.49033 6.68037
111 LEU 6.30 7.58888 6.72418
112 VAL 5.80 7.09610 6.50220
113 TRP 7.20 8.47589 7.10629
114 TYR 6.90 8.18022 6.98124
115 ALA 4.60 5.91342 5.93567
116 GLY 3.80 5.12496 5.52580
117 THR 5.60 6.89898 6.41125
118 SER 4.80 6.11053 6.03378
119 GLN 6.10 7.39177 6.63628
120 ASN 5.70 6.99754 6.45688
121 GLU 6.10 7.39177 6.63628
122 ASP 5.60 6.89898 6.41125
123 HIS 6.20 7.49033 6.68037
124 ARG 6.80 8.08167 6.93906
125 LYS 6.30 7.58888 6.72418
126 PRO 5.60 6.89898 6.41125
128 ============================== End of MD run setup =============================
131 Energy-term weights (unscaled):
133 WSCC= 1.000000 (SC-SC)
134 WSCP= 1.233150 (SC-p)
135 WELEC= 0.844760 (p-p electr)
136 WVDWPP= 0.231730 (p-p VDW)
137 WBOND= 1.000000 (stretching)
138 WANG= 0.629540 (bending)
139 WSCLOC= 0.105540 (SC local)
140 WTOR= 1.843160 (torsional)
141 WTORD= 1.265710 (double torsional)
142 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
143 WEL_LOC= 0.373570 (multi-body 3-rd order)
144 WCORR4= 0.192120 (multi-body 4th order)
145 WCORR5= 0.000000 (multi-body 5th order)
146 WCORR6= 0.000000 (multi-body 6th order)
147 WSCCOR= 0.000000 (back-scloc correlation)
148 WTURN3= 1.403230 (turns, 3rd order)
149 WTURN4= 0.646730 (turns, 4th order)
150 WTURN6= 0.000000 (turns, 6th order)
152 Hydrogen-bonding correlation between contact pairs of peptide groups
154 Scaling factor of 1,4 SC-p interactions: 0.400
155 General scaling factor of SC-p interactions: 1.000
157 Energy-term weights (scaled):
159 WSCC= 1.000000 (SC-SC)
160 WSCP= 1.233150 (SC-p)
161 WELEC= 0.844760 (p-p electr)
162 WVDWPP= 0.231730 (p-p VDW)
163 WBOND= 1.000000 (stretching)
164 WANG= 0.629540 (bending)
165 WSCLOC= 0.105540 (SC local)
166 WTOR= 1.843160 (torsional)
167 WTORD= 1.265710 (double torsional)
168 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
169 WEL_LOC= 0.373570 (multi-body 3-rd order)
170 WCORR4= 0.192120 (multi-body 4th order)
171 WCORR5= 0.000000 (multi-body 5th order)
172 WCORR6= 0.000000 (multi-body 6th order)
173 WSCCOR= 0.000000 (back-scloc correlatkion)
174 WTURN3= 1.403230 (turns, 3rd order)
175 WTURN4= 0.646730 (turns, 4th order)
176 WTURN6= 0.000000 (turns, 6th order)
177 Reference temperature for weights calculation: 300.000000000000
178 Parameters of the SS-bond potential:
179 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
180 11.0000000000000 AKCT 12.0000000000000
181 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
183 EBR -5.50000000000000
184 PDB data will be read from file ../../../1L2Y.pdb
186 Backbone and SC coordinates as read from the PDB
187 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
188 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
189 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
190 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
191 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
192 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
193 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
194 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
195 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
196 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
197 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
198 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
199 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
200 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
201 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
202 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
203 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
204 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
205 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
206 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
207 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
208 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
209 nsup= 20 nstart_sup= 2
233 Boundaries in phi angle sampling:
257 nsup= 20 nstart_sup= 2 nstart_seq= 2
258 NZ_START= 2 NZ_END= 21
260 Contact order: 0.308441558441558
261 Shifting contacts: 2 2
276 Extended chain initial geometry.
278 Geometry of the virtual chain.
279 Res d Theta Gamma Dsc Alpha Beta
280 D 1 0.000 0.000 0.000 0.000 0.000 0.000
281 ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000
282 LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
283 TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
284 ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
285 GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
286 TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
287 LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
288 LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
289 ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
290 GLY 11 3.800 90.000 180.000 0.000 110.000 -120.000
291 GLY 12 3.800 90.000 180.000 0.000 110.000 -120.000
292 PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
293 SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
294 SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
295 GLY 16 3.800 90.000 180.000 0.000 110.000 -120.000
296 ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
297 PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
298 PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
299 PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
300 SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
301 D 22 3.800 90.000 180.000 0.000 0.000 0.000
304 ********************************************************************************
305 Processor 0: end reading molecular data.
306 ********************************************************************************
309 Mesoscopic molecular dynamics (MD) calculation.
311 ********************************************************************************
314 ====================MD calculation start====================
315 Initial velocities randomly generated
317 0 0.02267 0.06282 -0.18129 0.00000 0.00000 0.00000
318 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
319 2 -0.36014 -0.22705 -0.00171 -0.06904 -0.02446 0.24778
320 3 0.27655 0.20645 0.14150 0.26200 0.15105 0.09342
321 4 0.10834 -0.11941 0.14712 0.10330 -0.09595 0.03277
322 5 0.05798 -0.08974 0.08325 0.03879 0.02648 -0.14707
323 6 0.01211 0.16444 -0.14711 -0.01628 0.11599 -0.16511
324 7 -0.01010 -0.05513 0.03662 -0.18958 0.06429 0.04531
325 8 -0.01799 0.13439 -0.04510 0.02318 0.10657 0.03722
326 9 -0.26458 -0.01929 0.09531 -0.22533 -0.17075 -0.04594
327 10 0.14062 -0.06051 -0.18363 0.20415 -0.15549 -0.17329
328 11 -0.14145 0.13159 -0.00733 0.00000 0.00000 0.00000
329 12 0.19745 -0.24261 0.01759 0.00000 0.00000 0.00000
330 13 -0.15305 0.28008 0.07251 0.06558 0.14824 0.10057
331 14 0.11104 -0.31941 0.15684 -0.02949 -0.09688 0.05398
332 15 0.14534 0.10342 -0.23754 -0.13923 0.07952 0.07655
333 16 -0.11969 0.14757 0.15002 0.00000 0.00000 0.00000
334 17 -0.09007 -0.15856 -0.20234 -0.07955 -0.08516 -0.10245
335 18 0.24139 0.09063 0.14043 -0.02074 0.10220 0.04907
336 19 -0.14354 -0.07226 -0.29143 -0.12408 -0.06855 -0.02978
337 20 0.28536 0.09023 0.56577 0.02348 0.16297 0.19270
338 21 0.00000 0.00000 0.00000 -0.13725 -0.06434 -0.21957
339 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
340 Calling the zero-angular momentum subroutine
341 vcm right after adjustment:
342 1.837610523517500E-017 -2.960594732333751E-018 9.596410511702503E-018
345 alpha-carbon coordinates centroid coordinates
347 D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
348 ASN( 2) 3.80000 0.00000 0.00000 3.64779 0.96674 1.37044
349 LEU( 3) 3.80000 -3.80000 0.00000 2.68687 -3.62474 -1.57795
350 TYR( 4) 7.60000 -3.80000 0.00000 7.37548 -2.37399 2.02147
351 ILE( 5) 7.60000 -7.60000 0.00000 6.58044 -7.43947 -1.44530
352 GLN( 6) 11.40000 -7.60000 0.00000 11.19753 -6.31407 1.82291
353 TRP( 7) 11.40000 -11.40000 0.00000 9.90453 -11.16454 -2.11994
354 LEU( 8) 15.20000 -11.40000 0.00000 15.02474 -10.28687 1.57795
355 LYS( 9) 15.20000 -15.20000 0.00000 13.74127 -14.97033 -2.06786
356 ASP( 10) 19.00000 -15.20000 0.00000 18.84553 -14.21890 1.39078
357 GLY( 11) 19.00000 -19.00000 0.00000 19.00000 -19.00000 0.00000
358 GLY( 12) 22.80000 -19.00000 0.00000 22.80000 -19.00000 0.00000
359 PRO( 13) 22.80000 -22.80000 0.00000 22.02787 -22.67843 -1.09456
360 SER( 14) 26.60000 -22.80000 0.00000 26.49606 -22.13981 0.93587
361 SER( 15) 26.60000 -26.60000 0.00000 25.93981 -26.49606 -0.93587
362 GLY( 16) 30.40000 -26.60000 0.00000 30.40000 -26.60000 0.00000
363 ARG( 17) 30.40000 -30.40000 0.00000 28.66629 -30.12703 -2.45767
364 PRO( 18) 34.20000 -30.40000 0.00000 34.07843 -29.62787 1.09456
365 PRO( 19) 34.20000 -34.20000 0.00000 33.42787 -34.07843 -1.09456
366 PRO( 20) 38.00000 -34.20000 0.00000 37.87843 -33.42787 1.09456
367 SER( 21) 38.00000 -38.00000 0.00000 37.33981 -37.89606 -0.93587
368 D ( 22) 41.80000 -38.00000 0.00000 41.80000 -38.00000 0.00000
370 Geometry of the virtual chain.
371 Res d Theta Gamma Dsc Alpha Beta
372 D 1 0.000 0.000 0.000 0.000 0.000 0.000
373 ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000
374 LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
375 TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
376 ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
377 GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
378 TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
379 LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
380 LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
381 ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
382 GLY 11 3.800 90.000 180.000 0.000 180.000 180.000
383 GLY 12 3.800 90.000 180.000 0.000 180.000 180.000
384 PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
385 SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
386 SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
387 GLY 16 3.800 90.000 180.000 0.000 180.000 180.000
388 ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
389 PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
390 PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
391 PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
392 SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
393 D 22 3.800 90.000 180.000 0.000 180.000 180.000
394 Potential energy and its components
396 Virtual-chain energies:
398 EVDW= -1.947821E+01 WEIGHT= 1.000000D+00 (SC-SC)
399 EVDW2= 2.387106E+01 WEIGHT= 1.233150D+00 (SC-p)
400 EES= -7.520330E+00 WEIGHT= 8.447600D-01 (p-p)
401 EVDWPP= -2.624923E+01 WEIGHT= 2.317300D-01 (p-p VDW)
402 ESTR= 1.118676E+02 WEIGHT= 1.000000D+00 (stretching)
403 EBE= -1.933948E+01 WEIGHT= 6.295400D-01 (bending)
404 ESC= 8.868295E+01 WEIGHT= 1.055400D-01 (SC local)
405 ETORS= 2.664535E-15 WEIGHT= 1.843160D+00 (torsional)
406 ETORSD= -2.547586E+00 WEIGHT= 1.265710D+00 (double torsional)
407 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
408 ECORR4= -4.501075E+00 WEIGHT= 1.921200D-01 (multi-body)
409 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
410 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
411 EELLO= 2.197932E+01 WEIGHT= 3.735700D-01 (electrostatic-local)
412 ETURN3= -1.258124E+00 WEIGHT= 1.403230D+00 (turns, 3rd order)
413 ETURN4= 9.498513E+00 WEIGHT= 6.467300D-01 (turns, 4th order)
414 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
415 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
416 EDIHC= 0.000000E+00 (dihedral angle constraints)
417 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
418 UCONST= 0.000000E+00 (Constraint energy)
419 ETOT= 1.150741E+02 (total)
422 Kinetic energy 3.16218E+01
423 potential energy 1.15074E+02
424 total energy 1.46696E+02
426 maximum acceleration 4.85027E+00
430 =================================== Timing ===================================
432 MD calculations setup: 1.17188E-02
433 Energy & gradient evaluation: 3.75566E+02
434 Stochastic MD setup: 0.00000E+00
435 Stochastic MD step setup: 0.00000E+00
436 MD steps: 4.51895E+02
439 ============================ End of MD calculation ===========================
440 CG processor 0 is finishing work.
441 Total wall clock time 457.273437500000 sec