1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1L2Y_REMD.inp
5 Output file : 1L2Y_REMD.out_GB000
7 Sidechain potential file :
8 /users/pk376/unres-git/unres/PARAM/scinter_GB.parm
9 SCp potential file : /users/pk376/unres-git/unres/PARAM/scp.parm
10 Electrostatic potential file :
11 /users/pk376/unres-git/unres/PARAM/electr_631Gdp.parm
12 Cumulant coefficient file :
13 /users/pk376/unres-git/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3
14 Torsional parameter file :
15 /users/pk376/unres-git/unres/PARAM/torsion_631Gdp.parm
16 Double torsional parameter file :
17 /users/pk376/unres-git/unres/PARAM/torsion_double_631Gdp.parm
18 SCCOR parameter file : /users/pk376/unres-git/unres/PARAM/sccor_pdb_shelly.dat
19 Bond & inertia constant file :
20 /users/pk376/unres-git/unres/PARAM/bond_AM1.parm
21 Bending parameter file :
22 /users/pk376/unres-git/unres/PARAM/theta_abinitio.parm
23 Rotamer parameter file :
24 /users/pk376/unres-git/unres/PARAM/rotamers_AM1_aura.10022007.parm
26 /users/pk376/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 Mon Jul 23 17:44:56 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
95 Berendsen bath calculation
96 Temperature: 300.00000
97 Coupling constant (tau): 1.00000
98 Momenta will be reset at zero every 1000 steps
99 Velocities will be reset at random every 10000 steps
101 ============================== End of MD run setup =============================
109 tlist 250.000000000000 260.000000000000 270.000000000000
110 280.000000000000 290.000000000000 300.000000000000
111 310.000000000000 320.000000000000 330.000000000000
112 340.000000000000 350.000000000000 360.000000000000
113 370.000000000000 380.000000000000 390.000000000000
118 Total number of replicas 16
120 ============================== End of REMD run setup =============================
123 Energy-term weights (unscaled):
125 WSCC= 1.000000 (SC-SC)
126 WSCP= 1.233150 (SC-p)
127 WELEC= 0.844760 (p-p electr)
128 WVDWPP= 0.231730 (p-p VDW)
129 WBOND= 1.000000 (stretching)
130 WANG= 0.629540 (bending)
131 WSCLOC= 0.105540 (SC local)
132 WTOR= 1.843160 (torsional)
133 WTORD= 1.265710 (double torsional)
134 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
135 WEL_LOC= 0.373570 (multi-body 3-rd order)
136 WCORR4= 0.192120 (multi-body 4th order)
137 WCORR5= 0.000000 (multi-body 5th order)
138 WCORR6= 0.000000 (multi-body 6th order)
139 WSCCOR= 0.000000 (back-scloc correlation)
140 WTURN3= 1.403230 (turns, 3rd order)
141 WTURN4= 0.646730 (turns, 4th order)
142 WTURN6= 0.000000 (turns, 6th order)
144 Hydrogen-bonding correlation between contact pairs of peptide groups
146 Scaling factor of 1,4 SC-p interactions: 0.400
147 General scaling factor of SC-p interactions: 1.000
149 Energy-term weights (scaled):
151 WSCC= 1.000000 (SC-SC)
152 WSCP= 1.233150 (SC-p)
153 WELEC= 0.844760 (p-p electr)
154 WVDWPP= 0.231730 (p-p VDW)
155 WBOND= 1.000000 (stretching)
156 WANG= 0.629540 (bending)
157 WSCLOC= 0.105540 (SC local)
158 WTOR= 1.843160 (torsional)
159 WTORD= 1.265710 (double torsional)
160 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
161 WEL_LOC= 0.373570 (multi-body 3-rd order)
162 WCORR4= 0.192120 (multi-body 4th order)
163 WCORR5= 0.000000 (multi-body 5th order)
164 WCORR6= 0.000000 (multi-body 6th order)
165 WSCCOR= 0.000000 (back-scloc correlatkion)
166 WTURN3= 1.403230 (turns, 3rd order)
167 WTURN4= 0.646730 (turns, 4th order)
168 WTURN6= 0.000000 (turns, 6th order)
169 Reference temperature for weights calculation: 300.000000000000
170 Parameters of the SS-bond potential:
171 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
172 11.0000000000000 AKCT 12.0000000000000
173 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
175 EBR -5.50000000000000
176 PDB data will be read from file ../../../../1L2Y.pdb
178 Backbone and SC coordinates as read from the PDB
179 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
180 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
181 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
182 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
183 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
184 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
185 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
186 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
187 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
188 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
189 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
190 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
191 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
192 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
193 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
194 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
195 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
196 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
197 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
198 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
199 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
200 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
201 nsup= 20 nstart_sup= 2
225 Boundaries in phi angle sampling:
249 nsup= 20 nstart_sup= 2 nstart_seq= 2
250 NZ_START= 2 NZ_END= 21
252 Contact order: 0.308441558441558
253 Shifting contacts: 2 2
269 +dist.constr 1 2 3 3.88 3.70E-02
271 +dist.constr 2 2 4 5.58 2.68E-02
273 +dist.constr 3 2 5 5.04 3.01E-02
275 +dist.constr 4 2 6 6.32 2.25E-02
277 +dist.constr 5 2 7 8.77 1.07E-02
279 +dist.constr 6 2 8 9.91 7.02E-03
281 +dist.constr 7 2 9 10.61 5.25E-03
283 +dist.constr 8 2 10 12.89 1.80E-03
285 +dist.constr 9 3 4 3.86 3.71E-02
287 +dist.constr 10 3 5 5.48 2.74E-02
289 +dist.constr 11 3 6 5.24 2.89E-02
291 +dist.constr 12 3 7 6.43 2.19E-02
293 +dist.constr 13 3 8 8.85 1.04E-02
295 +dist.constr 14 3 9 10.21 6.21E-03
297 +dist.constr 15 3 10 11.39 3.74E-03
299 +dist.constr 16 4 5 3.87 3.70E-02
301 +dist.constr 17 4 6 5.41 2.78E-02
303 +dist.constr 18 4 7 4.91 3.09E-02
305 +dist.constr 19 4 8 6.11 2.37E-02
307 +dist.constr 20 4 9 8.65 1.12E-02
309 +dist.constr 21 4 10 10.11 6.47E-03
311 +dist.constr 22 5 6 3.85 3.72E-02
313 +dist.constr 23 5 7 5.39 2.80E-02
315 +dist.constr 24 5 8 5.08 2.99E-02
317 +dist.constr 25 5 9 6.11 2.37E-02
319 +dist.constr 26 5 10 8.79 1.07E-02
321 +dist.constr 27 6 7 3.87 3.71E-02
323 +dist.constr 28 6 8 5.61 2.67E-02
325 +dist.constr 29 6 9 5.36 2.82E-02
327 +dist.constr 30 6 10 6.73 2.02E-02
329 +dist.constr 31 7 8 3.86 3.71E-02
331 +dist.constr 32 7 9 5.70 2.61E-02
333 +dist.constr 33 7 10 5.59 2.68E-02
335 +dist.constr 34 8 9 3.88 3.70E-02
337 +dist.constr 35 8 10 5.38 2.80E-02
339 +dist.constr 36 9 10 3.86 3.71E-02
340 +dist.constr 1 2 3 3.88 0.00 0 0.0
341 +dist.constr 2 2 4 5.58 0.00 0 0.0
342 +dist.constr 3 2 5 5.04 0.00 0 0.0
343 +dist.constr 4 2 6 6.32 0.00 0 0.0
344 +dist.constr 5 2 7 8.77 0.00 0 0.0
345 +dist.constr 6 2 8 9.91 0.00 0 0.0
346 +dist.constr 7 2 9 10.61 0.00 0 0.0
347 +dist.constr 8 2 10 12.89 0.00 0 0.0
348 +dist.constr 9 3 4 3.86 0.00 0 0.0
349 +dist.constr 10 3 5 5.48 0.00 0 0.0
350 +dist.constr 11 3 6 5.24 0.00 0 0.0
351 +dist.constr 12 3 7 6.43 0.00 0 0.0
352 +dist.constr 13 3 8 8.85 0.00 0 0.0
353 +dist.constr 14 3 9 10.21 0.00 0 0.0
354 +dist.constr 15 3 10 11.39 0.00 0 0.0
355 +dist.constr 16 4 5 3.87 0.00 0 0.0
356 +dist.constr 17 4 6 5.41 0.00 0 0.0
357 +dist.constr 18 4 7 4.91 0.00 0 0.0
358 +dist.constr 19 4 8 6.11 0.00 0 0.0
359 +dist.constr 20 4 9 8.65 0.00 0 0.0
360 +dist.constr 21 4 10 10.11 0.00 0 0.0
361 +dist.constr 22 5 6 3.85 0.00 0 0.0
362 +dist.constr 23 5 7 5.39 0.00 0 0.0
363 +dist.constr 24 5 8 5.08 0.00 0 0.0
364 +dist.constr 25 5 9 6.11 0.00 0 0.0
365 +dist.constr 26 5 10 8.79 0.00 0 0.0
366 +dist.constr 27 6 7 3.87 0.00 0 0.0
367 +dist.constr 28 6 8 5.61 0.00 0 0.0
368 +dist.constr 29 6 9 5.36 0.00 0 0.0
369 +dist.constr 30 6 10 6.73 0.00 0 0.0
370 +dist.constr 31 7 8 3.86 0.00 0 0.0
371 +dist.constr 32 7 9 5.70 0.00 0 0.0
372 +dist.constr 33 7 10 5.59 0.00 0 0.0
373 +dist.constr 34 8 9 3.88 0.00 0 0.0
374 +dist.constr 35 8 10 5.38 0.00 0 0.0
375 +dist.constr 36 9 10 3.86 0.00 0 0.0
377 Geometry of the virtual chain.
378 Res d Theta Gamma Dsc Alpha Beta
379 D 1 0.000 0.000 0.000 0.000 0.000 0.000
380 ASN 2 3.861 0.000 0.000 1.977 94.624 -178.093
381 LEU 3 3.876 92.239 0.000 2.195 102.878 -79.236
382 TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440
383 ILE 5 3.871 90.357 45.849 1.692 144.011 -104.516
384 GLN 6 3.846 89.090 55.194 2.338 170.986 -139.318
385 TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913
386 LEU 8 3.859 93.032 48.298 2.105 151.723 -105.899
387 LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960
388 ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646
389 GLY 11 3.891 89.908 56.679 0.000 0.000 0.000
390 GLY 12 3.864 100.181 -87.304 0.000 0.000 0.000
391 PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580
392 SER 14 3.876 89.537 4.261 1.267 144.515 -129.218
393 SER 15 3.875 91.815 66.108 1.262 161.047 -100.177
394 GLY 16 3.866 101.784 70.140 0.000 0.000 0.000
395 ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716
396 PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024
397 PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417
398 PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207
399 SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341
400 D 22 3.858 114.201 180.000 0.000 0.000 0.000
403 ********************************************************************************
404 Processor 0: end reading molecular data.
405 ********************************************************************************
408 The following 36 distance constraints have been imposed
409 1 2 3 0 3.87640 0.00000 0.03702
410 2 2 4 0 5.57666 0.00000 0.02684
411 3 2 5 0 5.03889 0.00000 0.03009
412 4 2 6 0 6.31641 0.00000 0.02251
413 5 2 7 0 8.76681 0.00000 0.01075
414 6 2 8 0 9.90813 0.00000 0.00702
415 7 2 9 0 10.61482 0.00000 0.00525
416 8 2 10 0 12.89033 0.00000 0.00180
417 9 3 4 0 3.86050 0.00000 0.03711
418 10 3 5 0 5.48434 0.00000 0.02740
419 11 3 6 0 5.23878 0.00000 0.02888
420 12 3 7 0 6.42590 0.00000 0.02189
421 13 3 8 0 8.85122 0.00000 0.01043
422 14 3 9 0 10.21149 0.00000 0.00621
423 15 3 10 0 11.38863 0.00000 0.00374
424 16 4 5 0 3.87147 0.00000 0.03705
425 17 4 6 0 5.41330 0.00000 0.02783
426 18 4 7 0 4.90831 0.00000 0.03088
427 19 4 8 0 6.10832 0.00000 0.02371
428 20 4 9 0 8.64580 0.00000 0.01121
429 21 4 10 0 10.11108 0.00000 0.00647
430 22 5 6 0 3.84558 0.00000 0.03720
431 23 5 7 0 5.38909 0.00000 0.02797
432 24 5 8 0 5.07567 0.00000 0.02987
433 25 5 9 0 6.11071 0.00000 0.02369
434 26 5 10 0 8.79273 0.00000 0.01065
435 27 6 7 0 3.86660 0.00000 0.03708
436 28 6 8 0 5.60509 0.00000 0.02667
437 29 6 9 0 5.35795 0.00000 0.02816
438 30 6 10 0 6.72791 0.00000 0.02022
439 31 7 8 0 3.85852 0.00000 0.03712
440 32 7 9 0 5.69883 0.00000 0.02611
441 33 7 10 0 5.58812 0.00000 0.02678
442 34 8 9 0 3.88180 0.00000 0.03699
443 35 8 10 0 5.37698 0.00000 0.02804
444 36 9 10 0 3.86099 0.00000 0.03711
445 Replica exchange molecular dynamics (REMD) calculation.
447 ********************************************************************************
451 MREMD 16 time before 5.078125000000000E-002
453 i2rep 1 2 3 4 5 6 7 8 9 10
455 i2set 1 1 1 1 1 1 1 1 1 1
457 i,j,il,il1,i_index(i,j,il,il1)
491 REMD Temperature: 250.00000
492 ====================MD calculation start====================
493 Initial velocities randomly generated
495 0 0.02069 0.05735 -0.16550 0.00000 0.00000 0.00000
496 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
497 2 -0.32876 -0.20726 -0.00156 -0.06303 -0.02233 0.22619
498 3 0.25246 0.18847 0.12917 0.23917 0.13789 0.08528
499 4 0.09890 -0.10900 0.13430 0.09430 -0.08759 0.02991
500 5 0.05293 -0.08192 0.07599 0.03541 0.02418 -0.13426
501 6 0.01106 0.15012 -0.13429 -0.01486 0.10588 -0.15072
502 7 -0.00922 -0.05032 0.03343 -0.17306 0.05869 0.04136
503 8 -0.01642 0.12268 -0.04117 0.02116 0.09728 0.03398
504 9 -0.24153 -0.01761 0.08700 -0.20570 -0.15587 -0.04194
505 10 0.12837 -0.05524 -0.16763 0.18636 -0.14195 -0.15819
506 11 -0.12912 0.12012 -0.00669 0.00000 0.00000 0.00000
507 12 0.18024 -0.22147 0.01606 0.00000 0.00000 0.00000
508 13 -0.13972 0.25567 0.06619 0.05987 0.13532 0.09181
509 14 0.10136 -0.29158 0.14318 -0.02692 -0.08844 0.04927
510 15 0.13268 0.09441 -0.21684 -0.12710 0.07259 0.06988
511 16 -0.10926 0.13472 0.13695 0.00000 0.00000 0.00000
512 17 -0.08222 -0.14474 -0.18471 -0.07262 -0.07774 -0.09353
513 18 0.22036 0.08274 0.12819 -0.01893 0.09330 0.04480
514 19 -0.13103 -0.06596 -0.26603 -0.11327 -0.06258 -0.02718
515 20 0.26050 0.08237 0.51647 0.02143 0.14877 0.17591
516 21 0.00000 0.00000 0.00000 -0.12529 -0.05874 -0.20044
517 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
518 Calling the zero-angular momentum subroutine
519 vcm right after adjustment:
520 2.021371575869251E-017 -1.735521049988750E-018 1.041312629993250E-017
523 alpha-carbon coordinates centroid coordinates
525 D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
526 ASN( 2) 3.86050 0.00000 0.00000 2.55159 1.47985 0.06557
527 LEU( 3) 4.01193 -3.87344 0.00000 3.96088 -4.50305 -2.10206
528 TYR( 4) 7.87243 -3.87344 0.00000 10.79652 -4.89021 -1.22632
529 ILE( 5) 7.89655 -1.17680 2.77774 7.76075 0.44675 2.31935
530 GLN( 6) 5.70141 -3.47509 4.94285 3.60888 -3.02771 5.88565
531 TRP( 7) 8.16996 -6.36206 4.22016 10.77228 -8.29798 2.61912
532 LEU( 8) 11.25658 -4.20989 5.07405 12.42370 -3.38205 3.52958
533 LYS( 9) 9.76612 -2.79308 8.36640 6.86736 -2.82804 9.12493
534 ASP( 10) 9.49962 -6.42561 9.64741 7.69328 -7.25489 9.53489
535 GLY( 11) 13.31647 -6.90493 9.06335 13.31647 -6.90493 9.06335
536 GLY( 12) 13.30671 -8.01769 5.36352 13.30671 -8.01769 5.36352
537 PRO( 13) 15.31165 -11.32992 5.02827 16.17763 -10.48298 4.32295
538 SER( 14) 15.75414 -11.41497 8.87760 16.77305 -10.71800 9.16233
539 SER( 15) 11.95328 -11.92981 9.42670 11.12717 -10.97987 9.51528
540 GLY( 16) 11.45094 -15.53878 8.13618 11.45094 -15.53878 8.13618
541 ARG( 17) 9.54906 -14.31220 5.00147 7.79760 -12.40573 7.22288
542 PRO( 18) 10.53690 -13.94710 1.26956 9.62009 -14.99504 1.15440
543 PRO( 19) 10.30439 -10.55356 -0.55592 11.52337 -10.99526 -1.06954
544 PRO( 20) 6.99735 -9.68439 -2.34313 7.03150 -8.66136 -1.39345
545 SER( 21) 7.20688 -9.78655 -6.20031 7.28380 -10.16020 -6.79638
546 D ( 22) 3.89984 -8.91739 -7.98752 3.89984 -8.91739 -7.98752
548 Geometry of the virtual chain.
549 Res d Theta Gamma Dsc Alpha Beta
550 D 1 0.000 0.000 0.000 0.000 0.000 0.000
551 ASN 2 3.861 0.000 0.000 1.977 94.624 -178.093
552 LEU 3 3.876 92.239 0.000 2.195 102.878 -79.236
553 TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440
554 ILE 5 3.871 90.357 45.849 1.692 144.011 -104.516
555 GLN 6 3.846 89.090 55.194 2.338 170.986 -139.318
556 TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913
557 LEU 8 3.859 93.032 48.298 2.105 151.723 -105.899
558 LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960
559 ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646
560 GLY 11 3.891 89.908 56.679 0.000 180.000 180.000
561 GLY 12 3.864 100.181 -87.304 0.000 180.000 180.000
562 PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580
563 SER 14 3.876 89.537 4.261 1.267 144.515 -129.218
564 SER 15 3.875 91.815 66.108 1.262 161.047 -100.177
565 GLY 16 3.866 101.784 70.140 0.000 180.000 180.000
566 ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716
567 PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024
568 PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417
569 PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207
570 SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341
571 D 22 3.858 114.201 180.000 0.000 180.000 180.000
572 Potential energy and its components
574 Virtual-chain energies:
576 EVDW= -1.798849E+01 WEIGHT= 1.000000D+00 (SC-SC)
577 EVDW2= 4.471415E+01 WEIGHT= 1.233150D+00 (SC-p)
578 EES= -9.165378E+01 WEIGHT= 9.459849D-01 (p-p)
579 EVDWPP= -3.362882E+01 WEIGHT= 2.317300D-01 (p-p VDW)
580 ESTR= 5.659036E+01 WEIGHT= 1.000000D+00 (stretching)
581 EBE= -5.669935E+00 WEIGHT= 6.295400D-01 (bending)
582 ESC= 1.734458E+02 WEIGHT= 1.055400D-01 (SC local)
583 ETORS= 1.479510E+01 WEIGHT= 2.064020D+00 (torsional)
584 ETORSD= 1.006444E+00 WEIGHT= 1.555350D+00 (double torsional)
585 EHPB= 2.258117E-31 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
586 ECORR4= -6.528803E+01 WEIGHT= 2.541120D-01 (multi-body)
587 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
588 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
589 EELLO= -4.012900E+00 WEIGHT= 4.590562D-01 (electrostatic-local)
590 ETURN3= 1.829789E+01 WEIGHT= 1.724339D+00 (turns, 3rd order)
591 ETURN4= 6.580750E-01 WEIGHT= 8.554124D-01 (turns, 4th order)
592 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
593 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
594 EDIHC= 0.000000E+00 (dihedral angle constraints)
595 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
596 UCONST= 0.000000E+00 (Constraint energy)
597 ETOT= 5.976608E+01 (total)
600 Kinetic energy 2.56370E+01
601 potential energy 5.97661E+01
602 total energy 8.54031E+01
604 maximum acceleration 1.97137E+00
606 Setup time 5.468750000000000E-002
607 Velocities reset to random values, time 1999.80
608 Velocities reset to random values, time 3999.80
609 Velocities reset to random values, time 5999.80
610 Velocities reset to random values, time 7999.80
611 Velocities reset to random values, time 9999.80
612 Velocities reset to random values, time 11999.80
613 Velocities reset to random values, time 13999.80
614 Velocities reset to random values, time 15999.80
615 Velocities reset to random values, time 17999.80
616 Velocities reset to random values, time 19999.80
617 REMD synchro at 100000
618 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
620 REMD gather times= 40.8046875000000 3.906250000000000E-003
621 REMD writing rst time= 0.000000000000000E+000
622 REMD writing traj time= 3.906250000000000E-003
624 ACC 1 250.00000 0.00000 1
625 ACC 2 260.00000 1.00000 1
626 ACC 3 270.00000 1.00000 1
627 ACC 4 280.00000 0.00000 1
628 ACC 5 290.00000 0.00000 1
629 ACC 6 300.00000 1.00000 1
630 ACC 7 310.00000 0.00000 1
631 ACC 8 320.00000 1.00000 1
632 ACC 9 330.00000 1.00000 1
633 ACC 10 340.00000 1.00000 1
634 ACC 11 350.00000 0.00000 1
635 ACC 12 360.00000 1.00000 1
636 ACC 13 370.00000 0.00000 1
637 ACC 14 380.00000 1.00000 1
638 ACC 15 390.00000 1.00000 1
639 REMD scatter time= 0.000000000000000E+000
640 REMD exchange time= 7.812500000000000E-003
641 Velocities reset to random values, time 21999.80
642 Velocities reset to random values, time 23999.80
643 Velocities reset to random values, time 25999.80
644 Velocities reset to random values, time 27999.80
645 Velocities reset to random values, time 29999.80
646 Velocities reset to random values, time 31999.80
647 Velocities reset to random values, time 33999.80
648 Velocities reset to random values, time 35999.80
649 Velocities reset to random values, time 37999.80
650 Velocities reset to random values, time 39999.80
651 REMD synchro at 200000
652 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
654 REMD gather times= 81.6015625000000 0.000000000000000E+000
655 REMD writing rst time= 0.000000000000000E+000
656 REMD writing traj time= 3.906250000000000E-003
658 ACC 1 250.00000 0.00000 2
659 ACC 2 260.00000 0.50000 2
660 ACC 3 270.00000 1.00000 2
661 ACC 4 280.00000 0.50000 2
662 ACC 5 290.00000 0.50000 2
663 ACC 6 300.00000 1.00000 2
664 ACC 7 310.00000 0.00000 2
665 ACC 8 320.00000 0.50000 2
666 ACC 9 330.00000 1.00000 2
667 ACC 10 340.00000 1.00000 2
668 ACC 11 350.00000 0.00000 2
669 ACC 12 360.00000 1.00000 2
670 ACC 13 370.00000 0.50000 2
671 ACC 14 380.00000 1.00000 2
672 ACC 15 390.00000 1.00000 2
673 REMD scatter time= 0.000000000000000E+000
674 REMD exchange time= 3.906250000000000E-003
675 Velocities reset to random values, time 41999.80
676 Velocities reset to random values, time 43999.80
677 Velocities reset to random values, time 45999.80
678 Velocities reset to random values, time 47999.80
679 Velocities reset to random values, time 49999.80
680 Velocities reset to random values, time 51999.80
681 Velocities reset to random values, time 53999.80
682 Velocities reset to random values, time 55999.80
683 Velocities reset to random values, time 57999.80
684 Velocities reset to random values, time 59999.80
685 REMD synchro at 300000
686 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
688 REMD gather times= 122.531250000000 0.000000000000000E+000
689 REMD writing rst time= 3.906250000000000E-003
690 REMD writing traj time= 3.906250000000000E-003
692 ACC 1 250.00000 0.33333 3
693 ACC 2 260.00000 0.33333 3
694 ACC 3 270.00000 1.00000 3
695 ACC 4 280.00000 0.33333 3
696 ACC 5 290.00000 0.66667 3
697 ACC 6 300.00000 1.00000 3
698 ACC 7 310.00000 0.00000 3
699 ACC 8 320.00000 0.33333 3
700 ACC 9 330.00000 1.00000 3
701 ACC 10 340.00000 1.00000 3
702 ACC 11 350.00000 0.33333 3
703 ACC 12 360.00000 0.66667 3
704 ACC 13 370.00000 0.66667 3
705 ACC 14 380.00000 1.00000 3
706 ACC 15 390.00000 1.00000 3
707 REMD scatter time= 0.000000000000000E+000
708 REMD exchange time= 7.812500000000000E-003
709 Velocities reset to random values, time 61999.80
710 Velocities reset to random values, time 63999.80
711 Velocities reset to random values, time 65999.80
712 Velocities reset to random values, time 67999.80
713 Velocities reset to random values, time 69999.80
714 Velocities reset to random values, time 71999.80
715 Velocities reset to random values, time 73999.80
716 Velocities reset to random values, time 75999.80
717 Velocities reset to random values, time 77999.80
718 Velocities reset to random values, time 79999.80
719 REMD synchro at 400000
720 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
722 REMD gather times= 163.546875000000 0.000000000000000E+000
723 REMD writing rst time= 3.906250000000000E-003
724 REMD writing traj time= 0.000000000000000E+000
726 ACC 1 250.00000 0.50000 4
727 ACC 2 260.00000 0.25000 4
728 ACC 3 270.00000 0.75000 4
729 ACC 4 280.00000 0.25000 4
730 ACC 5 290.00000 0.75000 4
731 ACC 6 300.00000 0.75000 4
732 ACC 7 310.00000 0.00000 4
733 ACC 8 320.00000 0.50000 4
734 ACC 9 330.00000 1.00000 4
735 ACC 10 340.00000 1.00000 4
736 ACC 11 350.00000 0.50000 4
737 ACC 12 360.00000 0.75000 4
738 ACC 13 370.00000 0.50000 4
739 ACC 14 380.00000 1.00000 4
740 ACC 15 390.00000 1.00000 4
741 REMD scatter time= 0.000000000000000E+000
742 REMD exchange time= 3.906250000000000E-003
743 Velocities reset to random values, time 81999.80
744 Velocities reset to random values, time 83999.80
745 Velocities reset to random values, time 85999.80
746 Velocities reset to random values, time 87999.80
747 Velocities reset to random values, time 89999.80
748 Velocities reset to random values, time 91999.80
749 Velocities reset to random values, time 93999.80
750 Velocities reset to random values, time 95999.80
751 Velocities reset to random values, time 97999.80
752 Velocities reset to random values, time 99999.80
753 REMD synchro at 500000
754 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
756 REMD gather times= 204.277343750000 0.000000000000000E+000
757 REMD writing rst time= 0.000000000000000E+000
758 REMD writing traj time= 3.906250000000000E-003
760 ACC 1 250.00000 0.40000 5
761 ACC 2 260.00000 0.40000 5
762 ACC 3 270.00000 0.80000 5
763 ACC 4 280.00000 0.40000 5
764 ACC 5 290.00000 0.80000 5
765 ACC 6 300.00000 0.60000 5
766 ACC 7 310.00000 0.00000 5
767 ACC 8 320.00000 0.60000 5
768 ACC 9 330.00000 1.00000 5
769 ACC 10 340.00000 1.00000 5
770 ACC 11 350.00000 0.60000 5
771 ACC 12 360.00000 0.80000 5
772 ACC 13 370.00000 0.60000 5
773 ACC 14 380.00000 1.00000 5
774 ACC 15 390.00000 1.00000 5
775 REMD scatter time= 0.000000000000000E+000
776 REMD exchange time= 3.906250000000000E-003
777 Velocities reset to random values, time 101999.80
778 Velocities reset to random values, time 103999.80
779 Velocities reset to random values, time 105999.80
780 Velocities reset to random values, time 107999.80
781 Velocities reset to random values, time 109999.80
782 Velocities reset to random values, time 111999.80
783 Velocities reset to random values, time 113999.80
784 Velocities reset to random values, time 115999.80
785 Velocities reset to random values, time 117999.80
786 Velocities reset to random values, time 119999.80
787 REMD synchro at 600000
788 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
790 REMD gather times= 245.050781250000 0.000000000000000E+000
791 REMD writing rst time= 3.906250000000000E-003
792 REMD writing traj time= 3.906250000000000E-003
794 ACC 1 250.00000 0.33333 6
795 ACC 2 260.00000 0.50000 6
796 ACC 3 270.00000 0.66667 6
797 ACC 4 280.00000 0.50000 6
798 ACC 5 290.00000 0.83333 6
799 ACC 6 300.00000 0.50000 6
800 ACC 7 310.00000 0.00000 6
801 ACC 8 320.00000 0.66667 6
802 ACC 9 330.00000 1.00000 6
803 ACC 10 340.00000 0.83333 6
804 ACC 11 350.00000 0.50000 6
805 ACC 12 360.00000 0.83333 6
806 ACC 13 370.00000 0.66667 6
807 ACC 14 380.00000 1.00000 6
808 ACC 15 390.00000 1.00000 6
809 REMD scatter time= 0.000000000000000E+000
810 REMD exchange time= 7.812500000000000E-003
811 Velocities reset to random values, time 121999.80
812 Velocities reset to random values, time 123999.80
813 Velocities reset to random values, time 125999.80
814 Velocities reset to random values, time 127999.80
815 Velocities reset to random values, time 129999.80
816 Velocities reset to random values, time 131999.80
817 Velocities reset to random values, time 133999.80
818 Velocities reset to random values, time 135999.80
819 Velocities reset to random values, time 137999.80
820 Velocities reset to random values, time 139999.80
821 REMD synchro at 700000
822 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
824 REMD gather times= 287.152343750000 0.000000000000000E+000
825 REMD writing rst time= 0.000000000000000E+000
826 REMD writing traj time= 7.812500000000000E-003
828 ACC 1 250.00000 0.28571 7
829 ACC 2 260.00000 0.57143 7
830 ACC 3 270.00000 0.71429 7
831 ACC 4 280.00000 0.42857 7
832 ACC 5 290.00000 0.85714 7
833 ACC 6 300.00000 0.42857 7
834 ACC 7 310.00000 0.14286 7
835 ACC 8 320.00000 0.57143 7
836 ACC 9 330.00000 1.00000 7
837 ACC 10 340.00000 0.85714 7
838 ACC 11 350.00000 0.57143 7
839 ACC 12 360.00000 0.85714 7
840 ACC 13 370.00000 0.57143 7
841 ACC 14 380.00000 1.00000 7
842 ACC 15 390.00000 0.85714 7
843 REMD scatter time= 0.000000000000000E+000
844 REMD exchange time= 7.812500000000000E-003
845 Velocities reset to random values, time 141999.80
846 Velocities reset to random values, time 143999.80
847 Velocities reset to random values, time 145999.80
848 Velocities reset to random values, time 147999.80
849 Velocities reset to random values, time 149999.80
850 Velocities reset to random values, time 151999.80
851 Velocities reset to random values, time 153999.80
852 Velocities reset to random values, time 155999.80
853 Velocities reset to random values, time 157999.80
854 Velocities reset to random values, time 159999.80
855 REMD synchro at 800000
856 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
858 REMD gather times= 328.453125000000 0.000000000000000E+000
859 REMD writing rst time= 3.906250000000000E-003
860 REMD writing traj time= 3.906250000000000E-003
862 ACC 1 250.00000 0.25000 8
863 ACC 2 260.00000 0.50000 8
864 ACC 3 270.00000 0.62500 8
865 ACC 4 280.00000 0.37500 8
866 ACC 5 290.00000 0.87500 8
867 ACC 6 300.00000 0.37500 8
868 ACC 7 310.00000 0.12500 8
869 ACC 8 320.00000 0.62500 8
870 ACC 9 330.00000 1.00000 8
871 ACC 10 340.00000 0.87500 8
872 ACC 11 350.00000 0.50000 8
873 ACC 12 360.00000 0.87500 8
874 ACC 13 370.00000 0.62500 8
875 ACC 14 380.00000 0.87500 8
876 ACC 15 390.00000 0.87500 8
877 REMD scatter time= 0.000000000000000E+000
878 REMD exchange time= 7.812500000000000E-003
879 Velocities reset to random values, time 161999.80
880 Velocities reset to random values, time 163999.80
881 Velocities reset to random values, time 165999.80
882 Velocities reset to random values, time 167999.80
883 Velocities reset to random values, time 169999.80
884 Velocities reset to random values, time 171999.80
885 Velocities reset to random values, time 173999.80
886 Velocities reset to random values, time 175999.80
887 Velocities reset to random values, time 177999.80
888 Velocities reset to random values, time 179999.80
889 REMD synchro at 900000
890 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
892 REMD gather times= 369.187500000000 0.000000000000000E+000
893 REMD writing rst time= 3.906250000000000E-003
894 REMD writing traj time= 0.000000000000000E+000
896 ACC 1 250.00000 0.33333 9
897 ACC 2 260.00000 0.44444 9
898 ACC 3 270.00000 0.66667 9
899 ACC 4 280.00000 0.33333 9
900 ACC 5 290.00000 0.88889 9
901 ACC 6 300.00000 0.44444 9
902 ACC 7 310.00000 0.11111 9
903 ACC 8 320.00000 0.55556 9
904 ACC 9 330.00000 1.00000 9
905 ACC 10 340.00000 0.88889 9
906 ACC 11 350.00000 0.44444 9
907 ACC 12 360.00000 0.88889 9
908 ACC 13 370.00000 0.55556 9
909 ACC 14 380.00000 0.88889 9
910 ACC 15 390.00000 0.88889 9
911 REMD scatter time= 0.000000000000000E+000
912 REMD exchange time= 3.906250000000000E-003
913 Velocities reset to random values, time 181999.80
914 Velocities reset to random values, time 183999.80
915 Velocities reset to random values, time 185999.80
916 Velocities reset to random values, time 187999.80
917 Velocities reset to random values, time 189999.80
918 Velocities reset to random values, time 191999.80
919 Velocities reset to random values, time 193999.80
920 Velocities reset to random values, time 195999.80
921 Velocities reset to random values, time 197999.80
922 Velocities reset to random values, time 199999.80
923 REMD synchro at 1000000
924 ntwx_cache 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
926 writing restart at the end of run
929 =================================== Timing ===================================
931 MD calculations setup: 3.90625E-03
932 Energy & gradient evaluation: 3.76590E+02
933 Stochastic MD setup: 0.00000E+00
934 Stochastic MD step setup: 0.00000E+00
935 MD steps: 4.10020E+02
938 ============================ End of MD calculation ===========================
939 CG processor 0 is finishing work.
940 Total wall clock time 410.074218750000 sec