1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1L2Y_NVE.inp
5 Output file : 1L2Y_NVE.out_GB000
7 Sidechain potential file : ../../../../PARAM/scinter_GB.parm
8 SCp potential file : ../../../../PARAM/scp.parm
9 Electrostatic potential file : ../../../../PARAM/electr_631Gdp.parm
10 Cumulant coefficient file :
11 ../../../../PARAM/fourier_opt.parm.1igd_hc_iter3_3
12 Torsional parameter file : ../../../../PARAM/torsion_631Gdp.parm
13 Double torsional parameter file : ../../../../PARAM/torsion_double_631Gdp.parm
14 SCCOR parameter file : ../../../../PARAM/rotcorr_AM1.parm
15 Bond & inertia constant file : ../../../../PARAM/bond_AM1.parm
16 Bending parameter file : ../../../../PARAM/theta_abinitio.parm
17 Rotamer parameter file :
18 ../../../../PARAM/rotamers_AM1_aura.10022007.parm
19 Threading database : ../../../../PARAM/patterns.cart
20 --------------------------------------------------------------------------------
21 ********************************************************************************
22 United-residue force field calculation - parallel job.
23 ********************************************************************************
24 ### LAST MODIFIED 11/03/09 1:19PM by czarek
25 ++++ Compile info ++++
26 Version 2.4 build 3228
27 compiled Thu Sep 23 07:36:26 2010
28 compiled by adam@matrix3.chem.cornell.edu
30 OS release: 2.6.27.25-170.2.72.fc10.x86_64
31 OS version: #1 SMP Sun Jun 21 18:39:34 EDT 2009
33 CPPFLAGS = -DPROCOR -DLINUX -DUNRES -DMP -DMPI ...
34 INSTALL_DIR = /users/software/mpich-1.2.7p1_int...
37 FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
38 FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...
39 FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include
40 FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...
41 BIN = ../bin/unres_Tc_procor_new_em64_nh_hremd_...
42 LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf_em64/l...
45 object = unres.o arcos.o cartprint.o chainbuild...
46 ++++ End of compile info ++++
48 Potential is GB , exponents are 6 12
50 Disulfide bridge parameters:
51 S-S bridge energy: -5.50
52 d0cm: 3.78 akcm: 15.10
53 akth: 11.00 akct: 12.00
54 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
55 MPI: node= 0 iseed= -3059742
56 ran_num 0.273754117333397
62 Time limit (min): 960.0
64 Library routine used to diagonalize matrices.
66 =========================== Parameters of the MD run ===========================
69 positions: angstrom, time: 48.9 fs
70 velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2
71 energy: kcal/mol, temperature: K
73 Number of time steps: 1000000
74 Initial time step of numerical integration: 0.10000 natural units
76 Maximum acceleration threshold to reduce the time step/increase split number:**********
77 Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000
78 Maximum velocity threshold to reduce velocities: 20.00000
79 Frequency of property output: 100
80 Frequency of coordinate output: 10000
81 Microcanonical mode calculation
83 ============================== End of MD run setup =============================
86 Energy-term weights (unscaled):
88 WSCC= 1.000000 (SC-SC)
90 WELEC= 0.844760 (p-p electr)
91 WVDWPP= 0.231730 (p-p VDW)
92 WBOND= 1.000000 (stretching)
93 WANG= 0.629540 (bending)
94 WSCLOC= 0.105540 (SC local)
95 WTOR= 1.843160 (torsional)
96 WTORD= 1.265710 (double torsional)
97 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
98 WEL_LOC= 0.373570 (multi-body 3-rd order)
99 WCORR4= 0.192120 (multi-body 4th order)
100 WCORR5= 0.000000 (multi-body 5th order)
101 WCORR6= 0.000000 (multi-body 6th order)
102 WSCCOR= 0.000000 (back-scloc correlation)
103 WTURN3= 1.403230 (turns, 3rd order)
104 WTURN4= 0.646730 (turns, 4th order)
105 WTURN6= 0.000000 (turns, 6th order)
107 Hydrogen-bonding correlation between contact pairs of peptide groups
109 Scaling factor of 1,4 SC-p interactions: 0.400
110 General scaling factor of SC-p interactions: 1.000
112 Energy-term weights (scaled):
114 WSCC= 1.000000 (SC-SC)
115 WSCP= 1.233150 (SC-p)
116 WELEC= 0.844760 (p-p electr)
117 WVDWPP= 0.231730 (p-p VDW)
118 WBOND= 1.000000 (stretching)
119 WANG= 0.629540 (bending)
120 WSCLOC= 0.105540 (SC local)
121 WTOR= 1.843160 (torsional)
122 WTORD= 1.265710 (double torsional)
123 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
124 WEL_LOC= 0.373570 (multi-body 3-rd order)
125 WCORR4= 0.192120 (multi-body 4th order)
126 WCORR5= 0.000000 (multi-body 5th order)
127 WCORR6= 0.000000 (multi-body 6th order)
128 WSCCOR= 0.000000 (back-scloc correlatkion)
129 WTURN3= 1.403230 (turns, 3rd order)
130 WTURN4= 0.646730 (turns, 4th order)
131 WTURN6= 0.000000 (turns, 6th order)
132 Reference temperature for weights calculation: 300.000000000000
133 Parameters of the SS-bond potential:
134 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
135 11.0000000000000 AKCT 12.0000000000000
136 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
138 EBR -5.50000000000000
139 PDB data will be read from file 1L2Y.pdb
141 Backbone and SC coordinates as read from the PDB
142 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
143 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
144 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
145 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
146 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
147 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
148 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
149 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
150 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
151 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
152 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
153 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
154 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
155 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
156 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
157 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
158 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
159 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
160 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
161 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
162 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
163 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
164 nsup= 20 nstart_sup= 2
188 Boundaries in phi angle sampling:
212 nsup= 20 nstart_sup= 2 nstart_seq= 2
213 NZ_START= 2 NZ_END= 21
215 Processor 0 CG group 0 absolute rank 0 nhpb
216 0 link_start= 1 link_end 0
217 Contact order: 0.308441558441558
218 Shifting contacts: 2 2
233 Initial geometry will be read in.
235 Geometry of the virtual chain.
236 Res d Theta Gamma Dsc Alpha Beta
237 D 1 0.000 0.000 0.000 0.000 0.000 0.000
238 ASN 2 3.800 0.000 0.000 2.008 102.356 -82.317
239 LEU 3 3.800 104.929 0.000 1.782 120.092 -56.685
240 TYR 4 3.800 87.695 -100.430 3.362 152.364 85.090
241 ILE 5 3.800 81.904 72.426 1.645 134.976 -88.666
242 GLN 6 3.800 82.466 66.026 2.125 122.343 -140.945
243 TRP 7 3.800 84.466 51.434 3.368 152.178 38.024
244 LEU 8 3.800 83.945 53.508 1.782 159.052 179.471
245 LYS 9 3.800 85.396 60.569 2.379 100.558 -73.090
246 ASP 10 3.800 91.449 44.177 2.030 139.961 -144.797
247 GLY 11 3.800 94.602 67.604 0.000 0.000 0.000
248 GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000
249 PRO 13 3.800 119.363 -61.916 1.422 117.453 -133.163
250 SER 14 3.800 94.363 -75.894 1.311 137.025 -106.659
251 SER 15 3.800 96.264 67.358 1.311 146.290 -130.305
252 GLY 16 3.800 138.119 129.701 0.000 0.000 0.000
253 ARG 17 3.800 96.299 -95.571 2.644 93.901 -102.747
254 PRO 18 3.800 129.702 63.972 1.422 101.025 -111.641
255 PRO 19 3.800 109.445 -74.504 1.422 113.043 -122.044
256 PRO 20 3.800 106.349 -122.306 1.422 93.778 -102.374
257 SER 21 3.800 106.042 -134.605 1.311 153.835 -143.303
258 D 22 3.800 108.718 92.113 0.000 0.000 0.000
261 ********************************************************************************
262 Processor 0: end reading molecular data.
263 ********************************************************************************
266 Mesoscopic molecular dynamics (MD) calculation.
268 ********************************************************************************
271 ====================MD calculation start====================
272 Initial velocities randomly generated
274 0 0.14116 0.06019 0.00651 0.00000 0.00000 0.00000
275 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
276 2 -0.17175 -0.01249 -0.15331 -0.02090 -0.05792 -0.09881
277 3 0.15276 0.01076 0.15619 -0.00869 -0.01649 0.14952
278 4 0.09714 0.21962 -0.00076 -0.13161 0.00105 -0.13191
279 5 -0.28995 -0.28661 -0.04399 -0.20794 -0.09712 0.06109
280 6 0.02606 -0.09397 0.00121 0.02142 0.02371 0.06777
281 7 0.14043 0.10719 0.11062 0.03017 0.12211 0.14888
282 8 -0.15894 0.05289 -0.04945 -0.08870 -0.06076 0.05527
283 9 0.00083 -0.06721 -0.12843 0.11538 -0.05179 -0.14286
284 10 0.29223 -0.07835 0.13064 0.07317 0.00083 0.11341
285 11 -0.41159 0.15104 -0.01780 0.00000 0.00000 0.00000
286 12 0.28145 -0.01326 0.08243 0.00000 0.00000 0.00000
287 13 -0.33623 0.09347 -0.10808 -0.02992 0.03048 -0.13246
288 14 0.40983 0.00917 -0.03051 0.24109 -0.19177 -0.02812
289 15 -0.14238 -0.04269 0.11329 -0.06397 -0.14551 -0.10490
290 16 -0.11159 -0.01629 0.01549 0.00000 0.00000 0.00000
291 17 0.08712 -0.04737 0.04618 0.02491 -0.13909 -0.04091
292 18 -0.17195 -0.14441 -0.13341 0.13324 -0.01700 -0.06373
293 19 0.13399 0.09745 -0.00585 0.01171 0.10181 -0.02391
294 20 -0.08296 -0.16674 0.16475 0.07397 -0.09732 -0.22217
295 21 0.00000 0.00000 0.00000 0.05726 0.10954 -0.06352
296 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
297 Calling the zero-angular momentum subroutine
298 vcm right after adjustment:
299 1.286327366462250E-017 -2.000953681163500E-017 1.837610523517500E-017
302 alpha-carbon coordinates centroid coordinates
304 D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
305 ASN( 2) 3.80000 0.00000 0.00000 4.26975 0.18095 1.94388
306 LEU( 3) 4.77894 -3.67174 0.00000 6.31901 -4.53513 -0.24135
307 TYR( 4) 5.40376 -3.34701 3.73419 7.55891 -4.78495 5.87678
308 ILE( 5) 1.60715 -3.20688 3.81267 0.73770 -2.09486 2.96799
309 GLN( 6) 1.94839 -6.79081 2.59652 1.68900 -6.04496 0.62369
310 TRP( 7) 4.28674 -7.18710 5.56554 6.59213 -8.78349 7.43105
311 LEU( 8) 1.35234 -5.80840 7.54758 1.63700 -4.28385 8.42522
312 LYS( 9) -0.53224 -8.86183 6.29662 -0.00767 -9.23195 4.00588
313 ASP( 10) 2.43549 -11.11658 7.03737 3.34686 -10.96549 5.22976
314 GLY( 11) 2.18504 -10.72111 10.80843 2.18504 -10.72111 10.80843
315 GLY( 12) 3.43786 -7.16826 11.30614 3.43786 -7.16826 11.30614
316 PRO( 13) 6.99461 -6.28836 10.29851 6.38906 -5.04979 9.95015
317 SER( 14) 8.57536 -7.97729 13.31326 8.27901 -7.31582 14.40566
318 SER( 15) 7.65918 -11.53050 12.32568 6.66212 -11.02899 11.63788
319 GLY( 16) 9.38152 -14.89751 11.95581 9.38152 -14.89751 11.95581
320 ARG( 17) 10.03694 -14.62275 8.22286 7.70563 -13.38339 8.36325
321 PRO( 18) 12.21420 -12.16088 6.31531 11.83401 -13.04317 5.26692
322 PRO( 19) 10.48638 -8.77881 6.18806 11.54928 -8.45202 7.07436
323 PRO( 20) 10.10763 -7.90895 2.50840 8.73829 -7.78513 2.87126
324 SER( 21) 11.17729 -4.27813 2.17220 10.19436 -3.61358 2.72982
325 D ( 22) 14.88269 -4.17086 1.33644 14.88269 -4.17086 1.33644
327 Geometry of the virtual chain.
328 Res d Theta Gamma Dsc Alpha Beta
329 D 1 0.000 0.000 0.000 0.000 0.000 0.000
330 ASN 2 3.800 0.000 0.000 2.008 102.356 -82.317
331 LEU 3 3.800 104.929 0.000 1.782 120.092 -56.685
332 TYR 4 3.800 87.695 -100.430 3.362 152.364 85.090
333 ILE 5 3.800 81.904 72.426 1.645 134.976 -88.666
334 GLN 6 3.800 82.466 66.026 2.125 122.343 -140.945
335 TRP 7 3.800 84.466 51.434 3.368 152.178 38.024
336 LEU 8 3.800 83.945 53.508 1.782 159.052 179.471
337 LYS 9 3.800 85.396 60.569 2.379 100.558 -73.090
338 ASP 10 3.800 91.449 44.177 2.030 139.961 -144.797
339 GLY 11 3.800 94.602 67.604 0.000 180.000 180.000
340 GLY 12 3.800 101.862 -72.814 0.000 180.000 180.000
341 PRO 13 3.800 119.363 -61.916 1.422 117.453 -133.163
342 SER 14 3.800 94.363 -75.894 1.311 137.025 -106.659
343 SER 15 3.800 96.264 67.358 1.311 146.290 -130.305
344 GLY 16 3.800 138.119 129.701 0.000 180.000 180.000
345 ARG 17 3.800 96.299 -95.571 2.644 93.901 -102.747
346 PRO 18 3.800 129.702 63.972 1.422 101.025 -111.641
347 PRO 19 3.800 109.445 -74.504 1.422 113.043 -122.045
348 PRO 20 3.800 106.349 -122.306 1.422 93.777 -102.374
349 SER 21 3.800 106.042 -134.605 1.311 153.835 -143.303
350 D 22 3.800 108.718 92.113 0.000 180.000 180.000
351 Potential energy and its components
353 Virtual-chain energies:
355 EVDW= -4.743995E+01 WEIGHT= 1.000000D+00 (SC-SC)
356 EVDW2= 5.228224E+01 WEIGHT= 1.233150D+00 (SC-p)
357 EES= -1.132072E+02 WEIGHT= 8.447600D-01 (p-p)
358 EVDWPP= 2.375178E+01 WEIGHT= 2.317300D-01 (p-p VDW)
359 ESTR= 8.998619E+00 WEIGHT= 1.000000D+00 (stretching)
360 EBE= -1.256949E+01 WEIGHT= 6.295400D-01 (bending)
361 ESC= 5.871725E+01 WEIGHT= 1.055400D-01 (SC local)
362 ETORS= 8.243370E+00 WEIGHT= 1.843160D+00 (torsional)
363 ETORSD= 2.390466E+00 WEIGHT= 1.265710D+00 (double torsional)
364 EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
365 ECORR4= -8.338619E+01 WEIGHT= 1.921200D-01 (multi-body)
366 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
367 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
368 EELLO= -5.753258E+00 WEIGHT= 3.735700D-01 (electrostatic-local)
369 ETURN3= 1.901845E+01 WEIGHT= 1.403230D+00 (turns, 3rd order)
370 ETURN4= -7.304754E+00 WEIGHT= 6.467300D-01 (turns, 4th order)
371 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
372 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
373 EDIHC= 0.000000E+00 (dihedral angle constraints)
374 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
375 UCONST= 0.000000E+00 (Constraint energy)
376 ETOT= -4.380127E+01 (total)
379 Kinetic energy 2.69321E+01
380 potential energy -4.38013E+01
381 total energy -1.68691E+01
383 maximum acceleration 2.54656E-01
387 =================================== Timing ===================================
389 MD calculations setup: 7.81250E-03
390 Energy & gradient evaluation: 2.39664E+02
391 Stochastic MD setup: 0.00000E+00
392 Stochastic MD step setup: 0.00000E+00
393 MD steps: 2.60770E+02
396 ============================ End of MD calculation ===========================
397 CG processor 0 is finishing work.
398 Total wall clock time 260.796875000000 sec