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lammps/examples/USER/colvars/log.peptide.4
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log.peptide.4
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LAMMPS (5 Mar 2012-ICMS)
using 4 OpenMP thread(s) per MPI task
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 MPI processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
84 atoms in group peptide
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
PPPM initialization ...
G vector (1/distance) = 0.268721
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.01614
estimated relative force accuracy = 4.86052e-05
using single precision FFTs
brick FFT buffer size/proc = 4312 960 3696
Last active /omp style is kspace_style pppm/omp
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-03.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 10
colvars: # colvarsRestartFrequency = 100
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out.colvars.state".
colvars: The trajectory file will be "out.colvars.traj".
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = groups_distance
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 3 initialized: total mass = 40.021.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 3 initialized: total mass = 3.024.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # upperWallConstant = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off
colvars: # outputAppliedForce = on
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = h_pot
colvars: # colvars = { groups_distance }
colvars: # forceConstant = 1000
colvars: # centers = { 1.78 }
colvars: # targetCenters = { 5 }
colvars: # targetForceConstant = 0 [default]
colvars: # targetNumSteps = 300
colvars: # targetNumStages = 0
colvars: # targetForceExponent = 1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars: ----------------------------------------------------------------------
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 11.9308 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26771.8055 E_long = -33907.4679 Press = -845.4762
SHAKE stats (type/ave/delta) on step 100
4 1.111 9.0854e-06
6 0.997 1.48942e-06
8 1.08 6.85613e-07
10 1.111 6.532e-07
12 1.08 2.94021e-07
14 0.96 0
18 0.957201 5.60693e-06
31 104.52 0.000513999
---------------- Step 100 ----- CPU = 0.3618 (sec) ----------------
TotEng = -5140.5516 KinEng = 1081.1161 Temp = 268.7271
PotEng = -6221.6677 E_bond = 47.0554 E_angle = 120.4842
E_dihed = 15.2364 E_impro = 2.1201 E_vdwl = 710.1878
E_coul = 26789.2822 E_long = -33906.0338 Press = -1670.9919
colvars: Writing the state file "rest.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
SHAKE stats (type/ave/delta) on step 200
4 1.11101 3.60095e-05
6 0.997 1.14983e-07
8 1.08 5.57449e-08
10 1.111 3.58012e-07
12 1.08 1.37945e-07
14 0.96 0
18 0.957201 3.23807e-06
31 104.52 0.000384411
---------------- Step 200 ----- CPU = 0.7253 (sec) ----------------
TotEng = -4815.6263 KinEng = 1098.1131 Temp = 272.9520
PotEng = -5913.7394 E_bond = 221.4543 E_angle = 312.1403
E_dihed = 16.6890 E_impro = 2.1985 E_vdwl = 675.6909
E_coul = 26761.7768 E_long = -33903.6892 Press = -4684.0335
colvars: Writing the state file "rest.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
SHAKE stats (type/ave/delta) on step 300
4 1.11101 3.69106e-05
6 0.997001 3.09063e-06
8 1.08 1.86488e-06
10 1.111 3.80862e-06
12 1.08 1.63097e-06
14 0.960001 0
18 0.957201 6.65746e-06
31 104.52 0.00066176
---------------- Step 300 ----- CPU = 1.0953 (sec) ----------------
TotEng = -4131.7404 KinEng = 1136.9353 Temp = 282.6018
PotEng = -5268.6757 E_bond = 574.2907 E_angle = 557.6703
E_dihed = 17.5023 E_impro = 1.5970 E_vdwl = 713.6254
E_coul = 26774.8501 E_long = -33908.2114 Press = -6069.5134
colvars: Writing the state file "rest.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
SHAKE stats (type/ave/delta) on step 400
4 1.11101 4.19727e-05
6 0.997 1.05072e-06
8 1.08 1.75272e-06
10 1.111 2.75019e-06
12 1.08 2.71371e-06
14 0.96 0
18 0.9572 8.73006e-06
31 104.52 0.00100388
---------------- Step 400 ----- CPU = 1.4662 (sec) ----------------
TotEng = -4193.0903 KinEng = 1092.0058 Temp = 271.4339
PotEng = -5285.0962 E_bond = 588.1062 E_angle = 545.6143
E_dihed = 16.6675 E_impro = 1.4911 E_vdwl = 727.0908
E_coul = 26745.4559 E_long = -33909.5219 Press = -5744.1190
colvars: Writing the state file "rest.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
SHAKE stats (type/ave/delta) on step 500
4 1.11101 4.51748e-05
6 0.997002 2.99571e-06
8 1.08 1.22925e-06
10 1.111 6.52473e-06
12 1.08 2.83498e-06
14 0.960003 0
18 0.957202 9.21962e-06
31 104.52 0.000887646
---------------- Step 500 ----- CPU = 2.1822 (sec) ----------------
TotEng = -4197.4061 KinEng = 1064.6756 Temp = 264.6406
PotEng = -5262.0817 E_bond = 568.5012 E_angle = 571.0415
E_dihed = 20.7146 E_impro = 0.6197 E_vdwl = 732.8477
E_coul = 26750.5832 E_long = -33906.3898 Press = -5923.5616
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 2.1822 on 16 procs (4 MPI x 4 OpenMP) for 500 steps with 2004 atoms
Performance: 39.593 ns/day 0.606 hours/ns 229.126 timesteps/s
Section | min time | avg time | max time |%total | #Thr
--------------------------------------------------------------
Pair | 0.97733 | 0.98935 | 1.0025 | 45.34 | 4.0x
Bond | 0.0051472 | 0.013997 | 0.02635 | 0.64 | 3.5x
Kspace | 0.49671 | 0.54112 | 0.56522 | 24.80 | 3.9x
Neigh | 0.1246 | 0.13284 | 0.14046 | 6.09 | 3.9x
Comm | 0.21512 | 0.27386 | 0.3074 | 12.55 | 3.9x
Output | 0.0002737 | 0.00028527 | 0.00031257 | 0.01 | 1.0x
Modify | 0.19386 | 0.22629 | 0.25635 | 10.37 | 3.9x
Other | | 0.004464 | | 0.20 |
FFT time (% of Kspce) = 0.0777066 (14.3605)
FFT Gflps 3d (1d only) = 3.52853 6.64761
Nlocal: 501 ave 514 max 494 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 6573.5 ave 6598 max 6544 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 176939 ave 181597 max 173450 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 707756
Ave neighs/atom = 353.172
Ave special neighs/atom = 2.34032
Neighbor list builds = 41
Dangerous builds = 0
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