1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1L2Y_MD.inp
5 Output file : 1L2Y_MD.out_GB000
7 Sidechain potential file :
8 /users/czarek/UNRES/export_v3/PARAM/scinter_GB.parm
9 SCp potential file : /users/czarek/UNRES/export_v3/PARAM/scp.parm
10 Electrostatic potential file :
11 /users/czarek/UNRES/export_v3/PARAM/electr_631Gdp.parm
12 Cumulant coefficient file :
13 /users/czarek/UNRES/export_v3/PARAM/fourier_opt.parm.1igd_hc_iter3_3
14 Torsional parameter file :
15 /users/czarek/UNRES/export_v3/PARAM/torsion_631Gdp.parm
16 Double torsional parameter file :
17 /users/czarek/UNRES/export_v3/PARAM/torsion_double_631Gdp.parm
18 SCCOR parameter file : /users/czarek/UNRES/export_v3/PARAM/rotcorr_AM1.parm
19 Bond & inertia constant file : /users/czarek/UNRES/export_v3/PARAM/bond.parm
20 Bending parameter file :
21 /users/czarek/UNRES/export_v3/PARAM/thetaml.5parm
22 Rotamer parameter file :
23 /users/czarek/UNRES/export_v3/PARAM/scgauss.parm
25 /users/czarek/UNRES/export_v3/PARAM/patterns.cart
26 --------------------------------------------------------------------------------
27 ********************************************************************************
28 United-residue force field calculation - parallel job.
29 ********************************************************************************
30 ### LAST MODIFIED 04/08/11 11:00AM by czarek
31 ++++ Compile info ++++
33 compiled Thu Dec 1 05:12:23 2011
34 compiled by czarek@matrix.chem.cornell.edu
36 OS release: 2.6.34.8-68.fc13.x86_64
37 OS version: #1 SMP Thu Feb 17 15:03:58 UTC 2011
39 CPPFLAGS = -DCRYST_BOND -DCRYST_THETA -DCRYST_S...
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 BIN = ../bin/unres_120111_mpich1_oldparm.exe
48 LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...
51 object = unres.o arcos.o cartprint.o chainbuild...
52 ++++ End of compile info ++++
54 Potential is GB , exponents are 6 12
56 Disulfide bridge parameters:
57 S-S bridge energy: -5.50
58 d0cm: 3.78 akcm: 15.10
59 akth: 11.00 akct: 12.00
60 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
61 MPI: node= 0 iseed= -3059742
62 ran_num 0.273754117333397
68 Time limit (min): 960.0
70 Library routine used to diagonalize matrices.
72 =========================== Parameters of the MD run ===========================
75 positions: angstrom, time: 48.9 fs
76 velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2
77 energy: kcal/mol, temperature: K
79 Number of time steps: 1000000
80 Initial time step of numerical integration: 0.20000 natural units
82 A-MTS algorithm used; initial time step for fast-varying short-range forces split into 1 steps.
83 Short-range force cutoff 2.00 lambda 0.30
84 Maximum acceleration threshold to reduce the time step/increase split number: 10.00000
85 Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000
86 Maximum velocity threshold to reduce velocities: 20.00000
87 Frequency of property output: 10000
88 Frequency of coordinate output: 10000
90 Langevin dynamics calculation with direct integration of Langevin equations
92 Temperature: 300.00000
93 Viscosity of the solvent: 0.89040
94 Radius of solvent molecule: 1.40000
95 Scaling factor of the friction forces: 0.02000
96 Eta of the solvent in natural units: 49.27846
98 Radii of site types and friction coefficients and std's of stochastic forces of fully exposed sites
100 p 5.00 6.30764 6.13033
101 CYS 5.00 6.30764 6.13033
102 MET 6.20 7.49033 6.68037
103 PHE 6.80 8.08167 6.93906
104 ILE 6.20 7.49033 6.68037
105 LEU 6.30 7.58888 6.72418
106 VAL 5.80 7.09610 6.50220
107 TRP 7.20 8.47589 7.10629
108 TYR 6.90 8.18022 6.98124
109 ALA 4.60 5.91342 5.93567
110 GLY 3.80 5.12496 5.52580
111 THR 5.60 6.89898 6.41125
112 SER 4.80 6.11053 6.03378
113 GLN 6.10 7.39177 6.63628
114 ASN 5.70 6.99754 6.45688
115 GLU 6.10 7.39177 6.63628
116 ASP 5.60 6.89898 6.41125
117 HIS 6.20 7.49033 6.68037
118 ARG 6.80 8.08167 6.93906
119 LYS 6.30 7.58888 6.72418
120 PRO 5.60 6.89898 6.41125
122 ============================== End of MD run setup =============================
125 Energy-term weights (unscaled):
127 WSCC= 1.352790 (SC-SC)
128 WSCP= 1.593040 (SC-p)
129 WELEC= 0.715340 (p-p electr)
130 WVDWPP= 0.113710 (p-p VDW)
131 WBOND= 1.000000 (stretching)
132 WANG= 1.138730 (bending)
133 WSCLOC= 0.162580 (SC local)
134 WTOR= 1.985990 (torsional)
135 WTORD= 1.570690 (double torsional)
136 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
137 WEL_LOC= 0.160360 (multi-body 3-rd order)
138 WCORR4= 0.428870 (multi-body 4th order)
139 WCORR5= 0.000000 (multi-body 5th order)
140 WCORR6= 0.000000 (multi-body 6th order)
141 WSCCOR= 0.000000 (back-scloc correlation)
142 WTURN3= 1.687220 (turns, 3rd order)
143 WTURN4= 0.662300 (turns, 4th order)
144 WTURN6= 0.000000 (turns, 6th order)
146 Hydrogen-bonding correlation between contact pairs of peptide groups
148 Scaling factor of 1,4 SC-p interactions: 0.400
149 General scaling factor of SC-p interactions: 1.000
151 Energy-term weights (scaled):
153 WSCC= 1.352790 (SC-SC)
154 WSCP= 1.593040 (SC-p)
155 WELEC= 0.715340 (p-p electr)
156 WVDWPP= 0.113710 (p-p VDW)
157 WBOND= 1.000000 (stretching)
158 WANG= 1.138730 (bending)
159 WSCLOC= 0.162580 (SC local)
160 WTOR= 1.985990 (torsional)
161 WTORD= 1.570690 (double torsional)
162 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
163 WEL_LOC= 0.160360 (multi-body 3-rd order)
164 WCORR4= 0.428870 (multi-body 4th order)
165 WCORR5= 0.000000 (multi-body 5th order)
166 WCORR6= 0.000000 (multi-body 6th order)
167 WSCCOR= 0.000000 (back-scloc correlatkion)
168 WTURN3= 1.687220 (turns, 3rd order)
169 WTURN4= 0.662300 (turns, 4th order)
170 WTURN6= 0.000000 (turns, 6th order)
171 Reference temperature for weights calculation: 300.000000000000
172 Parameters of the SS-bond potential:
173 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
174 11.0000000000000 AKCT 12.0000000000000
175 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
177 EBR -5.50000000000000
178 PDB data will be read from file ../../../1L2Y.pdb
180 Backbone and SC coordinates as read from the PDB
181 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
182 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
183 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
184 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
185 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
186 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
187 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
188 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
189 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
190 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
191 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
192 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
193 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
194 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
195 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
196 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
197 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
198 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
199 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
200 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
201 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
202 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
203 nsup= 20 nstart_sup= 2
227 Boundaries in phi angle sampling:
251 nsup= 20 nstart_sup= 2 nstart_seq= 2
252 NZ_START= 2 NZ_END= 21
254 Contact order: 0.308441558441558
255 Shifting contacts: 2 2
270 Extended chain initial geometry.
272 Geometry of the virtual chain.
273 Res d Theta Gamma Dsc Alpha Beta
274 D 1 0.000 0.000 0.000 0.000 0.000 0.000
275 ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000
276 LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
277 TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
278 ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
279 GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
280 TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
281 LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
282 LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
283 ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
284 GLY 11 3.800 90.000 180.000 0.000 110.000 -120.000
285 GLY 12 3.800 90.000 180.000 0.000 110.000 -120.000
286 PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
287 SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
288 SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
289 GLY 16 3.800 90.000 180.000 0.000 110.000 -120.000
290 ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
291 PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
292 PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
293 PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
294 SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
295 D 22 3.800 90.000 180.000 0.000 0.000 0.000
298 ********************************************************************************
299 Processor 0: end reading molecular data.
300 ********************************************************************************
303 Mesoscopic molecular dynamics (MD) calculation.
305 ********************************************************************************
308 ====================MD calculation start====================
309 Initial velocities randomly generated
311 0 0.14116 0.06019 0.00651 0.00000 0.00000 0.00000
312 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
313 2 -0.17175 -0.01249 -0.15331 -0.02090 -0.05792 -0.09881
314 3 0.15276 0.01076 0.15619 -0.00869 -0.01649 0.14952
315 4 0.09714 0.21962 -0.00076 -0.13161 0.00105 -0.13191
316 5 -0.28995 -0.28661 -0.04399 -0.20794 -0.09712 0.06109
317 6 0.02606 -0.09397 0.00121 0.02142 0.02371 0.06777
318 7 0.14043 0.10719 0.11062 0.03017 0.12211 0.14888
319 8 -0.15894 0.05289 -0.04945 -0.08870 -0.06076 0.05527
320 9 0.00083 -0.06721 -0.12843 0.11538 -0.05179 -0.14286
321 10 0.29223 -0.07835 0.13064 0.07317 0.00083 0.11341
322 11 -0.41159 0.15104 -0.01780 0.00000 0.00000 0.00000
323 12 0.28145 -0.01326 0.08243 0.00000 0.00000 0.00000
324 13 -0.33623 0.09347 -0.10808 -0.02992 0.03048 -0.13246
325 14 0.40983 0.00917 -0.03051 0.24109 -0.19177 -0.02812
326 15 -0.14238 -0.04269 0.11329 -0.06397 -0.14551 -0.10490
327 16 -0.11159 -0.01629 0.01549 0.00000 0.00000 0.00000
328 17 0.08712 -0.04737 0.04618 0.02491 -0.13909 -0.04091
329 18 -0.17195 -0.14441 -0.13341 0.13324 -0.01700 -0.06373
330 19 0.13399 0.09745 -0.00585 0.01171 0.10181 -0.02391
331 20 -0.08296 -0.16674 0.16475 0.07397 -0.09732 -0.22217
332 21 0.00000 0.00000 0.00000 0.05726 0.10954 -0.06352
333 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
334 Calling the zero-angular momentum subroutine
335 vcm right after adjustment:
336 2.057102891604313E-017 3.164773679391251E-017 -5.308652623495002E-018
339 alpha-carbon coordinates centroid coordinates
341 D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
342 ASN( 2) 3.80000 0.00000 0.00000 3.64779 0.96674 1.37044
343 LEU( 3) 3.80000 -3.80000 0.00000 2.68687 -3.62474 -1.57795
344 TYR( 4) 7.60000 -3.80000 0.00000 7.37548 -2.37399 2.02147
345 ILE( 5) 7.60000 -7.60000 0.00000 6.58044 -7.43947 -1.44530
346 GLN( 6) 11.40000 -7.60000 0.00000 11.19753 -6.31407 1.82291
347 TRP( 7) 11.40000 -11.40000 0.00000 9.90453 -11.16454 -2.11994
348 LEU( 8) 15.20000 -11.40000 0.00000 15.02474 -10.28687 1.57795
349 LYS( 9) 15.20000 -15.20000 0.00000 13.74127 -14.97033 -2.06786
350 ASP( 10) 19.00000 -15.20000 0.00000 18.84553 -14.21890 1.39078
351 GLY( 11) 19.00000 -19.00000 0.00000 19.00000 -19.00000 0.00000
352 GLY( 12) 22.80000 -19.00000 0.00000 22.80000 -19.00000 0.00000
353 PRO( 13) 22.80000 -22.80000 0.00000 22.02787 -22.67843 -1.09456
354 SER( 14) 26.60000 -22.80000 0.00000 26.49606 -22.13981 0.93587
355 SER( 15) 26.60000 -26.60000 0.00000 25.93981 -26.49606 -0.93587
356 GLY( 16) 30.40000 -26.60000 0.00000 30.40000 -26.60000 0.00000
357 ARG( 17) 30.40000 -30.40000 0.00000 28.66629 -30.12703 -2.45767
358 PRO( 18) 34.20000 -30.40000 0.00000 34.07843 -29.62787 1.09456
359 PRO( 19) 34.20000 -34.20000 0.00000 33.42787 -34.07843 -1.09456
360 PRO( 20) 38.00000 -34.20000 0.00000 37.87843 -33.42787 1.09456
361 SER( 21) 38.00000 -38.00000 0.00000 37.33981 -37.89606 -0.93587
362 D ( 22) 41.80000 -38.00000 0.00000 41.80000 -38.00000 0.00000
364 Geometry of the virtual chain.
365 Res d Theta Gamma Dsc Alpha Beta
366 D 1 0.000 0.000 0.000 0.000 0.000 0.000
367 ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000
368 LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
369 TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
370 ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
371 GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
372 TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
373 LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
374 LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
375 ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
376 GLY 11 3.800 90.000 180.000 0.000 180.000 180.000
377 GLY 12 3.800 90.000 180.000 0.000 180.000 180.000
378 PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
379 SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
380 SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
381 GLY 16 3.800 90.000 180.000 0.000 180.000 180.000
382 ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
383 PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
384 PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
385 PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
386 SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
387 D 22 3.800 90.000 180.000 0.000 180.000 180.000
388 Potential energy and its components
390 Virtual-chain energies:
392 EVDW= -1.947821E+01 WEIGHT= 1.352790D+00 (SC-SC)
393 EVDW2= 2.387106E+01 WEIGHT= 1.593040D+00 (SC-p)
394 EES= -7.520330E+00 WEIGHT= 7.153400D-01 (p-p)
395 EVDWPP= -2.624923E+01 WEIGHT= 1.137100D-01 (p-p VDW)
396 ESTR= 8.665144E-27 WEIGHT= 1.000000D+00 (stretching)
397 EBE= 1.082023E+00 WEIGHT= 1.138730D+00 (bending)
398 ESC= 9.168846E+01 WEIGHT= 1.625800D-01 (SC local)
399 ETORS= 2.664535E-15 WEIGHT= 1.985990D+00 (torsional)
400 ETORSD= -2.547586E+00 WEIGHT= 1.570690D+00 (double torsional)
401 EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
402 ECORR4= -4.501075E+00 WEIGHT= 4.288700D-01 (multi-body)
403 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
404 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
405 EELLO= 2.197932E+01 WEIGHT= 1.603600D-01 (electrostatic-local)
406 ETURN3= -1.258124E+00 WEIGHT= 1.687220D+00 (turns, 3rd order)
407 ETURN4= 9.498513E+00 WEIGHT= 6.623000D-01 (turns, 4th order)
408 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
409 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
410 EDIHC= 0.000000E+00 (dihedral angle constraints)
411 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
412 UCONST= 0.000000E+00 (Constraint energy)
413 ETOT= 2.121298E+01 (total)
416 Kinetic energy 2.60624E+01
417 potential energy 2.12130E+01
418 total energy 4.72754E+01
420 maximum acceleration 9.35162E-01
424 =================================== Timing ===================================
426 MD calculations setup: 7.81250E-03
427 Energy & gradient evaluation: 3.11953E+02
428 Stochastic MD setup: 0.00000E+00
429 Stochastic MD step setup: 0.00000E+00
430 MD steps: 3.65984E+02
433 ============================ End of MD calculation ===========================
434 CG processor 0 is finishing work.
435 Total wall clock time 373.972656250000 sec