1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1L2Y_MD.inp
5 Output file : 1L2Y_MD.out_GB000
7 Sidechain potential file :
8 /users/pk376/unres-git/unres/PARAM/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_ga
10 SCp potential file : /users/pk376/unres-git/unres/PARAM/scp.parm
11 Electrostatic potential file :
12 /users/pk376/unres-git/unres/PARAM/electr_631Gdp.parm
13 Cumulant coefficient file :
14 /users/pk376/unres-git/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3
15 Torsional parameter file :
16 /users/pk376/unres-git/unres/PARAM/torsion_631Gdp.parm
17 Double torsional parameter file :
18 /users/pk376/unres-git/unres/PARAM/torsion_double_631Gdp.parm
19 SCCOR parameter file : /users/pk376/unres-git/unres/PARAM/sccor_pdb_shelly.dat
20 Bond & inertia constant file : /users/pk376/unres-git/unres/PARAM/bond.parm
21 Bending parameter file :
22 /users/pk376/unres-git/unres/PARAM/thetaml.5parm
23 Rotamer parameter file :
24 /users/pk376/unres-git/unres/PARAM/scgauss.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 17:42:12 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 ++++
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 -46
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: 1000000
84 Initial time step of numerical integration: 0.10000 natural units
86 A-MTS algorithm used; initial time step for fast-varying short-range forces split into 1 steps.
87 Short-range force cutoff 2.00 lambda 0.30
88 Maximum acceleration threshold to reduce the time step/increase split number: 10.00000
89 Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000
90 Maximum velocity threshold to reduce velocities: 20.00000
91 Frequency of property output: 10000
92 Frequency of coordinate output: 10000
93 Nose-Hoover bath calculation
94 Mol.Phys. 87 1117 (1996) Martyna et al.
95 NVT-XI-RESPA algorithm
96 Temperature: 300.00000
99 ============================== End of MD run setup =============================
102 Energy-term weights (unscaled):
104 WSCC= 1.352790 (SC-SC)
105 WSCP= 1.593040 (SC-p)
106 WELEC= 0.715340 (p-p electr)
107 WVDWPP= 0.113710 (p-p VDW)
108 WBOND= 1.000000 (stretching)
109 WANG= 1.138730 (bending)
110 WSCLOC= 0.162580 (SC local)
111 WTOR= 1.985990 (torsional)
112 WTORD= 1.570690 (double torsional)
113 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
114 WEL_LOC= 0.160360 (multi-body 3-rd order)
115 WCORR4= 0.428870 (multi-body 4th order)
116 WCORR5= 0.000000 (multi-body 5th order)
117 WCORR6= 0.000000 (multi-body 6th order)
118 WSCCOR= 0.000000 (back-scloc correlation)
119 WTURN3= 1.687220 (turns, 3rd order)
120 WTURN4= 0.662300 (turns, 4th order)
121 WTURN6= 0.000000 (turns, 6th order)
123 Hydrogen-bonding correlation between contact pairs of peptide groups
125 Scaling factor of 1,4 SC-p interactions: 0.400
126 General scaling factor of SC-p interactions: 1.000
128 Energy-term weights (scaled):
130 WSCC= 1.352790 (SC-SC)
131 WSCP= 1.593040 (SC-p)
132 WELEC= 0.715340 (p-p electr)
133 WVDWPP= 0.113710 (p-p VDW)
134 WBOND= 1.000000 (stretching)
135 WANG= 1.138730 (bending)
136 WSCLOC= 0.162580 (SC local)
137 WTOR= 1.985990 (torsional)
138 WTORD= 1.570690 (double torsional)
139 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
140 WEL_LOC= 0.160360 (multi-body 3-rd order)
141 WCORR4= 0.428870 (multi-body 4th order)
142 WCORR5= 0.000000 (multi-body 5th order)
143 WCORR6= 0.000000 (multi-body 6th order)
144 WSCCOR= 0.000000 (back-scloc correlatkion)
145 WTURN3= 1.687220 (turns, 3rd order)
146 WTURN4= 0.662300 (turns, 4th order)
147 WTURN6= 0.000000 (turns, 6th order)
148 Reference temperature for weights calculation: 300.000000000000
149 Parameters of the SS-bond potential:
150 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
151 11.0000000000000 AKCT 12.0000000000000
152 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
154 EBR -5.50000000000000
155 PDB data will be read from file ../../../1L2Y.pdb
157 Backbone and SC coordinates as read from the PDB
158 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
159 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
160 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
161 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
162 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
163 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
164 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
165 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
166 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
167 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
168 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
169 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
170 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
171 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
172 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
173 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
174 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
175 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
176 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
177 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
178 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
179 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
180 nsup= 20 nstart_sup= 2
204 Boundaries in phi angle sampling:
228 nsup= 20 nstart_sup= 2 nstart_seq= 2
229 NZ_START= 2 NZ_END= 21
231 Contact order: 0.308441558441558
232 Shifting contacts: 2 2
247 Extended chain initial geometry.
249 Geometry of the virtual chain.
250 Res d Theta Gamma Dsc Alpha Beta
251 D 1 0.000 0.000 0.000 0.000 0.000 0.000
252 ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000
253 LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
254 TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
255 ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
256 GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
257 TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
258 LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
259 LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
260 ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
261 GLY 11 3.800 90.000 180.000 0.000 110.000 -120.000
262 GLY 12 3.800 90.000 180.000 0.000 110.000 -120.000
263 PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
264 SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
265 SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
266 GLY 16 3.800 90.000 180.000 0.000 110.000 -120.000
267 ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
268 PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
269 PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
270 PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
271 SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
272 D 22 3.800 90.000 180.000 0.000 0.000 0.000
275 ********************************************************************************
276 Processor 0: end reading molecular data.
277 ********************************************************************************
280 Mesoscopic molecular dynamics (MD) calculation.
282 ********************************************************************************
285 ====================MD calculation start====================
286 Initial velocities randomly generated
288 0 0.02267 0.06282 -0.18129 0.00000 0.00000 0.00000
289 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
290 2 -0.36014 -0.22705 -0.00171 -0.06904 -0.02446 0.24778
291 3 0.27655 0.20645 0.14150 0.26200 0.15105 0.09342
292 4 0.10834 -0.11941 0.14712 0.10330 -0.09595 0.03277
293 5 0.05798 -0.08974 0.08325 0.03879 0.02648 -0.14707
294 6 0.01211 0.16444 -0.14711 -0.01628 0.11599 -0.16511
295 7 -0.01010 -0.05513 0.03662 -0.18958 0.06429 0.04531
296 8 -0.01799 0.13439 -0.04510 0.02318 0.10657 0.03722
297 9 -0.26458 -0.01929 0.09531 -0.22533 -0.17075 -0.04594
298 10 0.14062 -0.06051 -0.18363 0.20415 -0.15549 -0.17329
299 11 -0.14145 0.13159 -0.00733 0.00000 0.00000 0.00000
300 12 0.19745 -0.24261 0.01759 0.00000 0.00000 0.00000
301 13 -0.15305 0.28008 0.07251 0.06558 0.14824 0.10057
302 14 0.11104 -0.31941 0.15684 -0.02949 -0.09688 0.05398
303 15 0.14534 0.10342 -0.23754 -0.13923 0.07952 0.07655
304 16 -0.11969 0.14757 0.15002 0.00000 0.00000 0.00000
305 17 -0.09007 -0.15856 -0.20234 -0.07955 -0.08516 -0.10245
306 18 0.24139 0.09063 0.14043 -0.02074 0.10220 0.04907
307 19 -0.14354 -0.07226 -0.29143 -0.12408 -0.06855 -0.02978
308 20 0.28536 0.09023 0.56577 0.02348 0.16297 0.19270
309 21 0.00000 0.00000 0.00000 -0.13725 -0.06434 -0.21957
310 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
311 Calling the zero-angular momentum subroutine
312 vcm right after adjustment:
313 1.837610523517500E-017 -2.960594732333751E-018 9.596410511702503E-018
316 alpha-carbon coordinates centroid coordinates
318 D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
319 ASN( 2) 3.80000 0.00000 0.00000 3.64779 0.96674 1.37044
320 LEU( 3) 3.80000 -3.80000 0.00000 2.68687 -3.62474 -1.57795
321 TYR( 4) 7.60000 -3.80000 0.00000 7.37548 -2.37399 2.02147
322 ILE( 5) 7.60000 -7.60000 0.00000 6.58044 -7.43947 -1.44530
323 GLN( 6) 11.40000 -7.60000 0.00000 11.19753 -6.31407 1.82291
324 TRP( 7) 11.40000 -11.40000 0.00000 9.90453 -11.16454 -2.11994
325 LEU( 8) 15.20000 -11.40000 0.00000 15.02474 -10.28687 1.57795
326 LYS( 9) 15.20000 -15.20000 0.00000 13.74127 -14.97033 -2.06786
327 ASP( 10) 19.00000 -15.20000 0.00000 18.84553 -14.21890 1.39078
328 GLY( 11) 19.00000 -19.00000 0.00000 19.00000 -19.00000 0.00000
329 GLY( 12) 22.80000 -19.00000 0.00000 22.80000 -19.00000 0.00000
330 PRO( 13) 22.80000 -22.80000 0.00000 22.02787 -22.67843 -1.09456
331 SER( 14) 26.60000 -22.80000 0.00000 26.49606 -22.13981 0.93587
332 SER( 15) 26.60000 -26.60000 0.00000 25.93981 -26.49606 -0.93587
333 GLY( 16) 30.40000 -26.60000 0.00000 30.40000 -26.60000 0.00000
334 ARG( 17) 30.40000 -30.40000 0.00000 28.66629 -30.12703 -2.45767
335 PRO( 18) 34.20000 -30.40000 0.00000 34.07843 -29.62787 1.09456
336 PRO( 19) 34.20000 -34.20000 0.00000 33.42787 -34.07843 -1.09456
337 PRO( 20) 38.00000 -34.20000 0.00000 37.87843 -33.42787 1.09456
338 SER( 21) 38.00000 -38.00000 0.00000 37.33981 -37.89606 -0.93587
339 D ( 22) 41.80000 -38.00000 0.00000 41.80000 -38.00000 0.00000
341 Geometry of the virtual chain.
342 Res d Theta Gamma Dsc Alpha Beta
343 D 1 0.000 0.000 0.000 0.000 0.000 0.000
344 ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000
345 LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
346 TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
347 ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
348 GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
349 TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
350 LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
351 LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
352 ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
353 GLY 11 3.800 90.000 180.000 0.000 180.000 180.000
354 GLY 12 3.800 90.000 180.000 0.000 180.000 180.000
355 PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
356 SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
357 SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
358 GLY 16 3.800 90.000 180.000 0.000 180.000 180.000
359 ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
360 PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
361 PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
362 PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
363 SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
364 D 22 3.800 90.000 180.000 0.000 180.000 180.000
366 Potential energy and its components
368 Virtual-chain energies:
370 EVDW= -1.680592E+01 WEIGHT= 1.352790D+00 (SC-SC)
371 EVDW2= 2.387106E+01 WEIGHT= 1.593040D+00 (SC-p)
372 EES= -7.520330E+00 WEIGHT= 7.153400D-01 (p-p)
373 EVDWPP= -2.624923E+01 WEIGHT= 1.137100D-01 (p-p VDW)
374 ESTR= 8.665144E-27 WEIGHT= 1.000000D+00 (stretching)
375 EBE= 1.082023E+00 WEIGHT= 1.138730D+00 (bending)
376 ESC= 9.168846E+01 WEIGHT= 1.625800D-01 (SC local)
377 ETORS= 2.664535E-15 WEIGHT= 1.985990D+00 (torsional)
378 ETORSD= -2.547586E+00 WEIGHT= 1.570690D+00 (double torsional)
379 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
380 ECORR4= -4.501075E+00 WEIGHT= 4.288700D-01 (multi-body)
381 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
382 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
383 EELLO= 2.197932E+01 WEIGHT= 1.603600D-01 (electrostatic-local)
384 ETURN3= -1.258124E+00 WEIGHT= 1.687220D+00 (turns, 3rd order)
385 ETURN4= 9.498513E+00 WEIGHT= 6.623000D-01 (turns, 4th order)
386 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
387 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
388 EDIHC= 0.000000E+00 (dihedral angle constraints)
389 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
390 UCONST= 0.000000E+00 (Constraint energy)
391 ETOT= 2.482802E+01 (total)
394 Kinetic energy 3.16218E+01
395 potential energy 2.48280E+01
396 total energy 5.64498E+01
398 maximum acceleration 7.07629E-01
400 acceleration/energy drift too large 11.2926424070625
401 13.6605134887925 split increased to 2 itime 5488
403 acceleration/energy drift too large 12.2479155916642
404 17.8916022742654 split increased to 2 itime 146134
406 acceleration/energy drift too large 9.64402968286842
407 11.3087438689470 split increased to 2 itime 173097
409 acceleration/energy drift too large 5.98151849708125
410 10.5358868963268 split increased to 2 itime 325094
412 acceleration/energy drift too large 9.92185743247020
413 10.3282402848183 split increased to 2 itime 337991
415 acceleration/energy drift too large 12.4467738353776
416 16.3475089599066 split increased to 2 itime 377718
418 acceleration/energy drift too large 9.40536271695775
419 11.7402473647113 split increased to 2 itime 399086
421 acceleration/energy drift too large 13.1653706876790
422 16.9150100267623 split increased to 2 itime 448471
424 acceleration/energy drift too large 6.46490539699288
425 12.1544022140714 split increased to 2 itime 477390
427 acceleration/energy drift too large 13.1589518405409
428 17.5436060457116 split increased to 2 itime 479111
430 acceleration/energy drift too large 10.5950744430222
431 10.4028358818328 split increased to 2 itime 479526
433 acceleration/energy drift too large 11.0521089342970
434 12.3123692023542 split increased to 2 itime 710277
436 acceleration/energy drift too large 5.83156435721131
437 10.6993564628405 split increased to 2 itime 739656
439 acceleration/energy drift too large 7.08760014331940
440 11.9290942024338 split increased to 2 itime 774367
442 acceleration/energy drift too large 12.2797621496046
443 17.4776170393841 split increased to 2 itime 906363
445 acceleration/energy drift too large 15.5956529698596
446 21.6103248292573 split increased to 2 itime 977004
450 =================================== Timing ===================================
452 MD calculations setup: 3.90625E-03
453 Energy & gradient evaluation: 3.74867E+02
454 Stochastic MD setup: 0.00000E+00
455 Stochastic MD step setup: 0.00000E+00
456 MD steps: 4.11719E+02
459 ============================ End of MD calculation ===========================
460 CG processor 0 is finishing work.
461 Total wall clock time 420.156250000000 sec