1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1L2Y_MD.inp
5 Output file : 1L2Y_MD.out_GB000
7 Sidechain potential file :
8 /users/adam/unres//PARAM/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_gap8g-sc
9 SCp potential file : /users/adam/unres//PARAM/scp.parm
10 Electrostatic potential file : /users/adam/unres//PARAM/electr_631Gdp.parm
11 Cumulant coefficient file :
12 /users/adam/unres//PARAM/fourier_opt.parm.1igd_hc_iter3_3
13 Torsional parameter file : /users/adam/unres//PARAM/torsion_631Gdp.parm
14 Double torsional parameter file :
15 /users/adam/unres//PARAM/torsion_double_631Gdp.parm
16 SCCOR parameter file : /users/adam/unres//PARAM/rotcorr_AM1.parm
17 Bond & inertia constant file : /users/adam/unres//PARAM/bond.parm
18 Bending parameter file : /users/adam/unres//PARAM/thetaml.5parm
19 Rotamer parameter file : /users/adam/unres//PARAM/scgauss.parm
20 Threading database : /users/adam/unres//PARAM/patterns.cart
21 --------------------------------------------------------------------------------
22 ********************************************************************************
23 United-residue force field calculation - parallel job.
24 ********************************************************************************
25 ### LAST MODIFIED 03/28/12 23:29 by czarek
26 ++++ Compile info ++++
28 compiled Sun May 13 16:07:22 2012
29 compiled by adam@matrix.chem.cornell.edu
31 OS release: 2.6.34.9-69.fc13.x86_64
32 OS version: #1 SMP Tue May 3 09:23:03 UTC 2011
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 LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...
44 object = unres.o arcos.o cartprint.o chainbuild...
45 GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...
46 GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP...
47 E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...
48 E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...
49 ++++ End of compile info ++++
51 Potential is GB , exponents are 6 12
53 Disulfide bridge parameters:
54 S-S bridge energy: -5.50
55 d0cm: 3.78 akcm: 15.10
56 akth: 11.00 akct: 12.00
57 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
58 MPI: node= 0 iseed(4)= 0 0 -46
60 ran_num 6.422640197456531E-013
66 Time limit (min): 960.0
68 Library routine used to diagonalize matrices.
70 =========================== Parameters of the MD run ===========================
73 positions: angstrom, time: 48.9 fs
74 velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2
75 energy: kcal/mol, temperature: K
77 Number of time steps: 1000000
78 Initial time step of numerical integration: 0.10000 natural units
80 A-MTS algorithm used; initial time step for fast-varying short-range forces split into 1 steps.
81 Short-range force cutoff 2.00 lambda 0.30
82 Maximum acceleration threshold to reduce the time step/increase split number: 10.00000
83 Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000
84 Maximum velocity threshold to reduce velocities: 20.00000
85 Frequency of property output: 10000
86 Frequency of coordinate output: 10000
87 Nose-Hoover bath calculation
88 Mol.Phys. 87 1117 (1996) Martyna et al.
89 NVT-XI-RESPA algorithm
90 Temperature: 300.00000
93 ============================== End of MD run setup =============================
96 Energy-term weights (unscaled):
98 WSCC= 1.352790 (SC-SC)
100 WELEC= 0.715340 (p-p electr)
101 WVDWPP= 0.113710 (p-p VDW)
102 WBOND= 1.000000 (stretching)
103 WANG= 1.138730 (bending)
104 WSCLOC= 0.162580 (SC local)
105 WTOR= 1.985990 (torsional)
106 WTORD= 1.570690 (double torsional)
107 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
108 WEL_LOC= 0.160360 (multi-body 3-rd order)
109 WCORR4= 0.428870 (multi-body 4th order)
110 WCORR5= 0.000000 (multi-body 5th order)
111 WCORR6= 0.000000 (multi-body 6th order)
112 WSCCOR= 0.000000 (back-scloc correlation)
113 WTURN3= 1.687220 (turns, 3rd order)
114 WTURN4= 0.662300 (turns, 4th order)
115 WTURN6= 0.000000 (turns, 6th order)
117 Hydrogen-bonding correlation between contact pairs of peptide groups
119 Scaling factor of 1,4 SC-p interactions: 0.400
120 General scaling factor of SC-p interactions: 1.000
122 Energy-term weights (scaled):
124 WSCC= 1.352790 (SC-SC)
125 WSCP= 1.593040 (SC-p)
126 WELEC= 0.715340 (p-p electr)
127 WVDWPP= 0.113710 (p-p VDW)
128 WBOND= 1.000000 (stretching)
129 WANG= 1.138730 (bending)
130 WSCLOC= 0.162580 (SC local)
131 WTOR= 1.985990 (torsional)
132 WTORD= 1.570690 (double torsional)
133 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
134 WEL_LOC= 0.160360 (multi-body 3-rd order)
135 WCORR4= 0.428870 (multi-body 4th order)
136 WCORR5= 0.000000 (multi-body 5th order)
137 WCORR6= 0.000000 (multi-body 6th order)
138 WSCCOR= 0.000000 (back-scloc correlatkion)
139 WTURN3= 1.687220 (turns, 3rd order)
140 WTURN4= 0.662300 (turns, 4th order)
141 WTURN6= 0.000000 (turns, 6th order)
142 Reference temperature for weights calculation: 300.000000000000
143 Parameters of the SS-bond potential:
144 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
145 11.0000000000000 AKCT 12.0000000000000
146 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
148 EBR -5.50000000000000
149 PDB data will be read from file ../../../1L2Y.pdb
151 Backbone and SC coordinates as read from the PDB
152 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
153 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
154 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
155 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
156 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
157 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
158 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
159 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
160 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
161 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
162 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
163 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
164 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
165 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
166 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
167 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
168 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
169 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
170 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
171 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
172 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
173 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
174 nsup= 20 nstart_sup= 2
198 Boundaries in phi angle sampling:
222 nsup= 20 nstart_sup= 2 nstart_seq= 2
223 NZ_START= 2 NZ_END= 21
225 Contact order: 0.308441558441558
226 Shifting contacts: 2 2
241 Extended chain initial geometry.
243 Geometry of the virtual chain.
244 Res d Theta Gamma Dsc Alpha Beta
245 D 1 0.000 0.000 0.000 0.000 0.000 0.000
246 ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000
247 LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
248 TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
249 ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
250 GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
251 TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
252 LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
253 LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
254 ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
255 GLY 11 3.800 90.000 180.000 0.000 110.000 -120.000
256 GLY 12 3.800 90.000 180.000 0.000 110.000 -120.000
257 PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
258 SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
259 SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
260 GLY 16 3.800 90.000 180.000 0.000 110.000 -120.000
261 ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
262 PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
263 PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
264 PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
265 SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
266 D 22 3.800 90.000 180.000 0.000 0.000 0.000
269 ********************************************************************************
270 Processor 0: end reading molecular data.
271 ********************************************************************************
274 Mesoscopic molecular dynamics (MD) calculation.
276 ********************************************************************************
279 ====================MD calculation start====================
280 Initial velocities randomly generated
282 0 0.02267 0.06282 -0.18129 0.00000 0.00000 0.00000
283 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
284 2 -0.36014 -0.22705 -0.00171 -0.06904 -0.02446 0.24778
285 3 0.27655 0.20645 0.14150 0.26200 0.15105 0.09342
286 4 0.10834 -0.11941 0.14712 0.10330 -0.09595 0.03277
287 5 0.05798 -0.08974 0.08325 0.03879 0.02648 -0.14707
288 6 0.01211 0.16444 -0.14711 -0.01628 0.11599 -0.16511
289 7 -0.01010 -0.05513 0.03662 -0.18958 0.06429 0.04531
290 8 -0.01799 0.13439 -0.04510 0.02318 0.10657 0.03722
291 9 -0.26458 -0.01929 0.09531 -0.22533 -0.17075 -0.04594
292 10 0.14062 -0.06051 -0.18363 0.20415 -0.15549 -0.17329
293 11 -0.14145 0.13159 -0.00733 0.00000 0.00000 0.00000
294 12 0.19745 -0.24261 0.01759 0.00000 0.00000 0.00000
295 13 -0.15305 0.28008 0.07251 0.06558 0.14824 0.10057
296 14 0.11104 -0.31941 0.15684 -0.02949 -0.09688 0.05398
297 15 0.14534 0.10342 -0.23754 -0.13923 0.07952 0.07655
298 16 -0.11969 0.14757 0.15002 0.00000 0.00000 0.00000
299 17 -0.09007 -0.15856 -0.20234 -0.07955 -0.08516 -0.10245
300 18 0.24139 0.09063 0.14043 -0.02074 0.10220 0.04907
301 19 -0.14354 -0.07226 -0.29143 -0.12408 -0.06855 -0.02978
302 20 0.28536 0.09023 0.56577 0.02348 0.16297 0.19270
303 21 0.00000 0.00000 0.00000 -0.13725 -0.06434 -0.21957
304 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
305 Calling the zero-angular momentum subroutine
306 vcm right after adjustment:
307 3.226027363508501E-017 2.674744206453251E-017 6.125368411725002E-018
310 alpha-carbon coordinates centroid coordinates
312 D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
313 ASN( 2) 3.80000 0.00000 0.00000 3.64779 0.96674 1.37044
314 LEU( 3) 3.80000 -3.80000 0.00000 2.68687 -3.62474 -1.57795
315 TYR( 4) 7.60000 -3.80000 0.00000 7.37548 -2.37399 2.02147
316 ILE( 5) 7.60000 -7.60000 0.00000 6.58044 -7.43947 -1.44530
317 GLN( 6) 11.40000 -7.60000 0.00000 11.19753 -6.31407 1.82291
318 TRP( 7) 11.40000 -11.40000 0.00000 9.90453 -11.16454 -2.11994
319 LEU( 8) 15.20000 -11.40000 0.00000 15.02474 -10.28687 1.57795
320 LYS( 9) 15.20000 -15.20000 0.00000 13.74127 -14.97033 -2.06786
321 ASP( 10) 19.00000 -15.20000 0.00000 18.84553 -14.21890 1.39078
322 GLY( 11) 19.00000 -19.00000 0.00000 19.00000 -19.00000 0.00000
323 GLY( 12) 22.80000 -19.00000 0.00000 22.80000 -19.00000 0.00000
324 PRO( 13) 22.80000 -22.80000 0.00000 22.02787 -22.67843 -1.09456
325 SER( 14) 26.60000 -22.80000 0.00000 26.49606 -22.13981 0.93587
326 SER( 15) 26.60000 -26.60000 0.00000 25.93981 -26.49606 -0.93587
327 GLY( 16) 30.40000 -26.60000 0.00000 30.40000 -26.60000 0.00000
328 ARG( 17) 30.40000 -30.40000 0.00000 28.66629 -30.12703 -2.45767
329 PRO( 18) 34.20000 -30.40000 0.00000 34.07843 -29.62787 1.09456
330 PRO( 19) 34.20000 -34.20000 0.00000 33.42787 -34.07843 -1.09456
331 PRO( 20) 38.00000 -34.20000 0.00000 37.87843 -33.42787 1.09456
332 SER( 21) 38.00000 -38.00000 0.00000 37.33981 -37.89606 -0.93587
333 D ( 22) 41.80000 -38.00000 0.00000 41.80000 -38.00000 0.00000
335 Geometry of the virtual chain.
336 Res d Theta Gamma Dsc Alpha Beta
337 D 1 0.000 0.000 0.000 0.000 0.000 0.000
338 ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000
339 LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
340 TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
341 ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
342 GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
343 TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
344 LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
345 LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
346 ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
347 GLY 11 3.800 90.000 180.000 0.000 180.000 180.000
348 GLY 12 3.800 90.000 180.000 0.000 180.000 180.000
349 PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
350 SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
351 SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
352 GLY 16 3.800 90.000 180.000 0.000 180.000 180.000
353 ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
354 PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
355 PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
356 PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
357 SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
358 D 22 3.800 90.000 180.000 0.000 180.000 180.000
360 Potential energy and its components
362 Virtual-chain energies:
364 EVDW= -1.680592E+01 WEIGHT= 1.352790D+00 (SC-SC)
365 EVDW2= 2.387106E+01 WEIGHT= 1.593040D+00 (SC-p)
366 EES= -7.520330E+00 WEIGHT= 7.153400D-01 (p-p)
367 EVDWPP= -2.624923E+01 WEIGHT= 1.137100D-01 (p-p VDW)
368 ESTR= 8.665144E-27 WEIGHT= 1.000000D+00 (stretching)
369 EBE= 1.082023E+00 WEIGHT= 1.138730D+00 (bending)
370 ESC= 9.168846E+01 WEIGHT= 1.625800D-01 (SC local)
371 ETORS= 2.664535E-15 WEIGHT= 1.985990D+00 (torsional)
372 ETORSD= -2.547586E+00 WEIGHT= 1.570690D+00 (double torsional)
373 EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
374 ECORR4= -4.501075E+00 WEIGHT= 4.288700D-01 (multi-body)
375 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
376 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
377 EELLO= 2.197932E+01 WEIGHT= 1.603600D-01 (electrostatic-local)
378 ETURN3= -1.258124E+00 WEIGHT= 1.687220D+00 (turns, 3rd order)
379 ETURN4= 9.498513E+00 WEIGHT= 6.623000D-01 (turns, 4th order)
380 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
381 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
382 EDIHC= 0.000000E+00 (dihedral angle constraints)
383 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
384 UCONST= 0.000000E+00 (Constraint energy)
385 ETOT= 2.482802E+01 (total)
388 Kinetic energy 3.16218E+01
389 potential energy 2.48280E+01
390 total energy 5.64498E+01
392 maximum acceleration 7.07629E-01
394 acceleration/energy drift too large 9.78013718448949
395 10.6971139128278 split increased to 2 itime 72745
397 acceleration/energy drift too large 6.65467285428532
398 11.4261305813792 split increased to 2 itime 213434
400 acceleration/energy drift too large 6.23173521323265
401 12.7765218283068 split increased to 2 itime 224643
403 acceleration/energy drift too large 9.82326621220746
404 10.5112359366962 split increased to 2 itime 240810
406 acceleration/energy drift too large 11.6741711355468
407 14.5266567820789 split increased to 2 itime 293410
409 acceleration/energy drift too large 14.4639213800120
410 23.7234928069806 split increased to 2 itime 413671
412 acceleration/energy drift too large 10.7495418233675
413 11.7766241585679 split increased to 2 itime 707772
415 acceleration/energy drift too large 14.1580222958177
416 15.5950126123075 split increased to 2 itime 782746
418 acceleration/energy drift too large 11.1422328063867
419 12.5552272072498 split increased to 2 itime 851609
421 acceleration/energy drift too large 7.92906617031973
422 14.0128676820342 split increased to 2 itime 904403
424 acceleration/energy drift too large 10.7058448136198
425 14.3424550573967 split increased to 2 itime 908867
429 =================================== Timing ===================================
431 MD calculations setup: 3.90625E-03
432 Energy & gradient evaluation: 3.09223E+02
433 Stochastic MD setup: 0.00000E+00
434 Stochastic MD step setup: 0.00000E+00
435 MD steps: 3.28801E+02
438 ============================ End of MD calculation ===========================
439 CG processor 0 is finishing work.
440 Total wall clock time 333.972656250000 sec