I don;t think I specified the problem well. This is a part of the output:

# Conjugate gradients optimization # Step Current energy Av shift Mx shift Funcs Gradient 0 127763.69531 0.0000 0.0000 1 5.80191e+06 9 1023.20831 0.0001 0.0013 27 7958.03 # Conjugate gradients optimization # Step Current energy Av shift Mx shift Funcs Gradient 0 10585.82617 0.0000 0.0000 1 798323 10 3038.98022 0.0422 0.5213 21 44036.2 20 1562.34656 0.0573 0.4620 41 21124.6 30 952.08020 0.0387 0.3051 61 6975.25 40 718.60651 0.0190 0.1223 81 2768.92 50 613.78882 0.0165 0.1318 101 1072.04 60 558.44568 0.0191 0.1931 121 844.107 70 528.58771 0.0160 0.1610 142 623.547 80 505.49722 0.0071 0.0432 162 182.543 90 488.25266 0.0116 0.0833 182 371.858 100 472.90448 0.0159 0.2190 202 199.59 110 464.42642 0.0060 0.0553 222 123.018 120 459.06067 0.0065 0.0453 242 74.0072 127 456.91678 0.0008 0.0088 258 27.1187 # Conjugate gradients optimization # Step Current energy Av shift Mx shift Funcs Gradient 0 2565.44043 0.0000 0.0000 1 872.504 1 2564.90918 0.0005 0.0043 3 776.596 # Conjugate gradients optimization

(...)

I was asking about the Conjugate gradients optimization initializations (each step of adding additional restraints), not about the steps of one CG process.

slow = schedule(4, [ step(CG, 2, mk_scale(default=0.01, nonbond=0.0)), step(CG, 4, mk_scale(default=0.10, nonbond=0.0)), step(CG, 6, mk_scale(default=0.50, nonbond=0.0)) ] + \ [ step(CG, rng, mk_scale(default=1.00, nonbond=0.0)) for rng in \ (8,10,14,18,20,24,30,25,40,45,50,55,60,70,80,90,100,120,140,160,200, 250,300,400,500) ] + \ [ step(CG, 600, mk_scale(default=1.00, nonbond=0.01)), step(CG, 800, mk_scale(default=1.00, nonbond=0.1)), step(CG, 1000, mk_scale(default=1.00, nonbond=0.5)), step(CG, 9999, physical.values(default=1.00)) ])

Number of steps from the script above is 32 (I understand, that those are the steps of each CG initializations), while CG initializations is smaller. I'm not asking about for example 9 steps of individual CG process from the top of the encolsed log fragment.

Dnia 31-05-2012 o godz. 19:17 Modeller Caretaker modeller-care@salilab.org napisał(a): > On 5/31/12 9:53 AM, M wrote: > > While analysing the log file of the optimization proces (X.D00000001) > > I've discovered, that the number of steps is different than the > > number from the applied schedule. What is the cause? > > See http://salilab.org/modeller/9.10/manual/node258.html, in particular > the description of the min_atom_shift parameter. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage