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 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: 0.10000 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 Nose-Hoover bath calculation
96 Mol.Phys. 87 1117 (1996) Martyna et al.
97 NVT-XI-RESPA algorithm
98 Temperature: 300.00000
101 ============================== End of MD run setup =============================
104 Energy-term weights (unscaled):
106 WSCC= 1.000000 (SC-SC)
107 WSCP= 1.233150 (SC-p)
108 WELEC= 0.844760 (p-p electr)
109 WVDWPP= 0.231730 (p-p VDW)
110 WBOND= 1.000000 (stretching)
111 WANG= 0.629540 (bending)
112 WSCLOC= 0.105540 (SC local)
113 WTOR= 1.843160 (torsional)
114 WTORD= 1.265710 (double torsional)
115 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
116 WEL_LOC= 0.373570 (multi-body 3-rd order)
117 WCORR4= 0.192120 (multi-body 4th order)
118 WCORR5= 0.000000 (multi-body 5th order)
119 WCORR6= 0.000000 (multi-body 6th order)
120 WSCCOR= 0.000000 (back-scloc correlation)
121 WTURN3= 1.403230 (turns, 3rd order)
122 WTURN4= 0.646730 (turns, 4th order)
123 WTURN6= 0.000000 (turns, 6th order)
125 Hydrogen-bonding correlation between contact pairs of peptide groups
127 Scaling factor of 1,4 SC-p interactions: 0.400
128 General scaling factor of SC-p interactions: 1.000
130 Energy-term weights (scaled):
132 WSCC= 1.000000 (SC-SC)
133 WSCP= 1.233150 (SC-p)
134 WELEC= 0.844760 (p-p electr)
135 WVDWPP= 0.231730 (p-p VDW)
136 WBOND= 1.000000 (stretching)
137 WANG= 0.629540 (bending)
138 WSCLOC= 0.105540 (SC local)
139 WTOR= 1.843160 (torsional)
140 WTORD= 1.265710 (double torsional)
141 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
142 WEL_LOC= 0.373570 (multi-body 3-rd order)
143 WCORR4= 0.192120 (multi-body 4th order)
144 WCORR5= 0.000000 (multi-body 5th order)
145 WCORR6= 0.000000 (multi-body 6th order)
146 WSCCOR= 0.000000 (back-scloc correlatkion)
147 WTURN3= 1.403230 (turns, 3rd order)
148 WTURN4= 0.646730 (turns, 4th order)
149 WTURN6= 0.000000 (turns, 6th order)
150 Reference temperature for weights calculation: 300.000000000000
151 Parameters of the SS-bond potential:
152 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
153 11.0000000000000 AKCT 12.0000000000000
154 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
156 EBR -5.50000000000000
157 PDB data will be read from file ../../../1L2Y.pdb
159 Backbone and SC coordinates as read from the PDB
160 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
161 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
162 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
163 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
164 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
165 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
166 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
167 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
168 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
169 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
170 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
171 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
172 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
173 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
174 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
175 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
176 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
177 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
178 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
179 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
180 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
181 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
182 nsup= 20 nstart_sup= 2
206 Boundaries in phi angle sampling:
230 nsup= 20 nstart_sup= 2 nstart_seq= 2
231 NZ_START= 2 NZ_END= 21
233 Contact order: 0.308441558441558
234 Shifting contacts: 2 2
249 Extended chain initial geometry.
251 Geometry of the virtual chain.
252 Res d Theta Gamma Dsc Alpha Beta
253 D 1 0.000 0.000 0.000 0.000 0.000 0.000
254 ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000
255 LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
256 TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
257 ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
258 GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
259 TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
260 LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
261 LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
262 ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
263 GLY 11 3.800 90.000 180.000 0.000 110.000 -120.000
264 GLY 12 3.800 90.000 180.000 0.000 110.000 -120.000
265 PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
266 SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
267 SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
268 GLY 16 3.800 90.000 180.000 0.000 110.000 -120.000
269 ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
270 PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
271 PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
272 PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
273 SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
274 D 22 3.800 90.000 180.000 0.000 0.000 0.000
277 ********************************************************************************
278 Processor 0: end reading molecular data.
279 ********************************************************************************
282 Mesoscopic molecular dynamics (MD) calculation.
284 ********************************************************************************
287 ====================MD calculation start====================
288 Initial velocities randomly generated
290 0 0.02267 0.06282 -0.18129 0.00000 0.00000 0.00000
291 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
292 2 -0.36014 -0.22705 -0.00171 -0.06904 -0.02446 0.24778
293 3 0.27655 0.20645 0.14150 0.26200 0.15105 0.09342
294 4 0.10834 -0.11941 0.14712 0.10330 -0.09595 0.03277
295 5 0.05798 -0.08974 0.08325 0.03879 0.02648 -0.14707
296 6 0.01211 0.16444 -0.14711 -0.01628 0.11599 -0.16511
297 7 -0.01010 -0.05513 0.03662 -0.18958 0.06429 0.04531
298 8 -0.01799 0.13439 -0.04510 0.02318 0.10657 0.03722
299 9 -0.26458 -0.01929 0.09531 -0.22533 -0.17075 -0.04594
300 10 0.14062 -0.06051 -0.18363 0.20415 -0.15549 -0.17329
301 11 -0.14145 0.13159 -0.00733 0.00000 0.00000 0.00000
302 12 0.19745 -0.24261 0.01759 0.00000 0.00000 0.00000
303 13 -0.15305 0.28008 0.07251 0.06558 0.14824 0.10057
304 14 0.11104 -0.31941 0.15684 -0.02949 -0.09688 0.05398
305 15 0.14534 0.10342 -0.23754 -0.13923 0.07952 0.07655
306 16 -0.11969 0.14757 0.15002 0.00000 0.00000 0.00000
307 17 -0.09007 -0.15856 -0.20234 -0.07955 -0.08516 -0.10245
308 18 0.24139 0.09063 0.14043 -0.02074 0.10220 0.04907
309 19 -0.14354 -0.07226 -0.29143 -0.12408 -0.06855 -0.02978
310 20 0.28536 0.09023 0.56577 0.02348 0.16297 0.19270
311 21 0.00000 0.00000 0.00000 -0.13725 -0.06434 -0.21957
312 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
313 Calling the zero-angular momentum subroutine
314 vcm right after adjustment:
315 1.837610523517500E-017 -2.960594732333751E-018 9.596410511702503E-018
318 alpha-carbon coordinates centroid coordinates
320 D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
321 ASN( 2) 3.80000 0.00000 0.00000 3.64779 0.96674 1.37044
322 LEU( 3) 3.80000 -3.80000 0.00000 2.68687 -3.62474 -1.57795
323 TYR( 4) 7.60000 -3.80000 0.00000 7.37548 -2.37399 2.02147
324 ILE( 5) 7.60000 -7.60000 0.00000 6.58044 -7.43947 -1.44530
325 GLN( 6) 11.40000 -7.60000 0.00000 11.19753 -6.31407 1.82291
326 TRP( 7) 11.40000 -11.40000 0.00000 9.90453 -11.16454 -2.11994
327 LEU( 8) 15.20000 -11.40000 0.00000 15.02474 -10.28687 1.57795
328 LYS( 9) 15.20000 -15.20000 0.00000 13.74127 -14.97033 -2.06786
329 ASP( 10) 19.00000 -15.20000 0.00000 18.84553 -14.21890 1.39078
330 GLY( 11) 19.00000 -19.00000 0.00000 19.00000 -19.00000 0.00000
331 GLY( 12) 22.80000 -19.00000 0.00000 22.80000 -19.00000 0.00000
332 PRO( 13) 22.80000 -22.80000 0.00000 22.02787 -22.67843 -1.09456
333 SER( 14) 26.60000 -22.80000 0.00000 26.49606 -22.13981 0.93587
334 SER( 15) 26.60000 -26.60000 0.00000 25.93981 -26.49606 -0.93587
335 GLY( 16) 30.40000 -26.60000 0.00000 30.40000 -26.60000 0.00000
336 ARG( 17) 30.40000 -30.40000 0.00000 28.66629 -30.12703 -2.45767
337 PRO( 18) 34.20000 -30.40000 0.00000 34.07843 -29.62787 1.09456
338 PRO( 19) 34.20000 -34.20000 0.00000 33.42787 -34.07843 -1.09456
339 PRO( 20) 38.00000 -34.20000 0.00000 37.87843 -33.42787 1.09456
340 SER( 21) 38.00000 -38.00000 0.00000 37.33981 -37.89606 -0.93587
341 D ( 22) 41.80000 -38.00000 0.00000 41.80000 -38.00000 0.00000
343 Geometry of the virtual chain.
344 Res d Theta Gamma Dsc Alpha Beta
345 D 1 0.000 0.000 0.000 0.000 0.000 0.000
346 ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000
347 LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
348 TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
349 ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
350 GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
351 TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
352 LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
353 LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
354 ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
355 GLY 11 3.800 90.000 180.000 0.000 180.000 180.000
356 GLY 12 3.800 90.000 180.000 0.000 180.000 180.000
357 PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
358 SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
359 SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
360 GLY 16 3.800 90.000 180.000 0.000 180.000 180.000
361 ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
362 PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
363 PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
364 PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
365 SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
366 D 22 3.800 90.000 180.000 0.000 180.000 180.000
368 Potential energy and its components
370 Virtual-chain energies:
372 EVDW= -1.947821E+01 WEIGHT= 1.000000D+00 (SC-SC)
373 EVDW2= 2.387106E+01 WEIGHT= 1.233150D+00 (SC-p)
374 EES= -7.520330E+00 WEIGHT= 8.447600D-01 (p-p)
375 EVDWPP= -2.624923E+01 WEIGHT= 2.317300D-01 (p-p VDW)
376 ESTR= 1.118676E+02 WEIGHT= 1.000000D+00 (stretching)
377 EBE= -1.933948E+01 WEIGHT= 6.295400D-01 (bending)
378 ESC= 8.868295E+01 WEIGHT= 1.055400D-01 (SC local)
379 ETORS= 2.664535E-15 WEIGHT= 1.843160D+00 (torsional)
380 ETORSD= -2.547586E+00 WEIGHT= 1.265710D+00 (double torsional)
381 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
382 ECORR4= -4.501075E+00 WEIGHT= 1.921200D-01 (multi-body)
383 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
384 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
385 EELLO= 2.197932E+01 WEIGHT= 3.735700D-01 (electrostatic-local)
386 ETURN3= -1.258124E+00 WEIGHT= 1.403230D+00 (turns, 3rd order)
387 ETURN4= 9.498513E+00 WEIGHT= 6.467300D-01 (turns, 4th order)
388 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
389 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
390 EDIHC= 0.000000E+00 (dihedral angle constraints)
391 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
392 UCONST= 0.000000E+00 (Constraint energy)
393 ETOT= 1.150741E+02 (total)
396 Kinetic energy 3.16218E+01
397 potential energy 1.15074E+02
398 total energy 1.46696E+02
400 maximum acceleration 4.85027E+00
404 =================================== Timing ===================================
406 MD calculations setup: 4.29688E-02
407 Energy & gradient evaluation: 3.69449E+02
408 Stochastic MD setup: 0.00000E+00
409 Stochastic MD step setup: 0.00000E+00
410 MD steps: 4.14484E+02
413 ============================ End of MD calculation ===========================
414 CG processor 0 is finishing work.
415 Total wall clock time 419.515625000000 sec