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gromacs-lysozyme

mahmoodn
Feb 28th, 2018
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  1. Log file opened on Wed Feb 28 19:23:23 2018
  2. Host: orca pid: 3773 rank ID: 0 number of ranks: 1
  3. :-) GROMACS - gmx mdrun, 2018 (-:
  4.  
  5. GROMACS is written by:
  6. Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
  7. Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
  8. Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
  9. Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
  10. Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff
  11. Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
  12. Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
  13. Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
  14. and the project leaders:
  15. Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
  16.  
  17. Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  18. Copyright (c) 2001-2017, The GROMACS development team at
  19. Uppsala University, Stockholm University and
  20. the Royal Institute of Technology, Sweden.
  21. check out http://www.gromacs.org for more information.
  22.  
  23. GROMACS is free software; you can redistribute it and/or modify it
  24. under the terms of the GNU Lesser General Public License
  25. as published by the Free Software Foundation; either version 2.1
  26. of the License, or (at your option) any later version.
  27.  
  28. GROMACS: gmx mdrun, version 2018
  29. Executable: /usr/local/gromacs/bin/gmx
  30. Data prefix: /usr/local/gromacs
  31. Working dir: /home/mahmood/gromacs-2018/bench/lysozyme
  32. Command line:
  33. gmx mdrun -nobackup -nb gpu -deffnm md_0_1
  34.  
  35. GROMACS version: 2018
  36. Precision: single
  37. Memory model: 64 bit
  38. MPI library: thread_mpi
  39. OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
  40. GPU support: CUDA
  41. SIMD instructions: AVX2_128
  42. FFT library: fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512
  43. RDTSCP usage: enabled
  44. TNG support: enabled
  45. Hwloc support: disabled
  46. Tracing support: disabled
  47. Built on: 2018-02-23 17:10:06
  48. Built by: mahmood@orca [CMAKE]
  49. Build OS/arch: Linux 4.10.0-28-generic x86_64
  50. Build CPU vendor: AMD
  51. Build CPU brand: AMD Ryzen 7 1800X Eight-Core Processor
  52. Build CPU family: 23 Model: 1 Stepping: 1
  53. Build CPU features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
  54. C compiler: /usr/bin/cc GNU 5.4.0
  55. C compiler flags: -march=core-avx2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
  56. C++ compiler: /usr/bin/c++ GNU 5.4.0
  57. C++ compiler flags: -march=core-avx2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
  58. CUDA compiler: /usr/local/cuda-9.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2017 NVIDIA Corporation;Built on Fri_Sep__1_21:08:03_CDT_2017;Cuda compilation tools, release 9.0, V9.0.176
  59. CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_70,code=compute_70;-use_fast_math;-D_FORCE_INLINES;; ;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
  60. CUDA driver: 9.0
  61. CUDA runtime: 9.0
  62.  
  63.  
  64. Running on 1 node with total 16 cores, 16 logical cores, 1 compatible GPU
  65. Hardware detected:
  66. CPU info:
  67. Vendor: AMD
  68. Brand: AMD Ryzen 7 1800X Eight-Core Processor
  69. Family: 23 Model: 1 Stepping: 1
  70. Features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
  71. Hardware topology: Basic
  72. Sockets, cores, and logical processors:
  73. Socket 0: [ 0] [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13] [ 14] [ 15]
  74. GPU info:
  75. Number of GPUs detected: 1
  76. #0: NVIDIA Quadro M2000, compute cap.: 5.2, ECC: no, stat: compatible
  77.  
  78.  
  79. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  80. M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
  81. Lindahl
  82. GROMACS: High performance molecular simulations through multi-level
  83. parallelism from laptops to supercomputers
  84. SoftwareX 1 (2015) pp. 19-25
  85. -------- -------- --- Thank You --- -------- --------
  86.  
  87.  
  88. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  89. S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
  90. Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
  91. GROMACS
  92. In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
  93. -------- -------- --- Thank You --- -------- --------
  94.  
  95.  
  96. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  97. S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
  98. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
  99. GROMACS 4.5: a high-throughput and highly parallel open source molecular
  100. simulation toolkit
  101. Bioinformatics 29 (2013) pp. 845-54
  102. -------- -------- --- Thank You --- -------- --------
  103.  
  104.  
  105. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  106. B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
  107. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
  108. molecular simulation
  109. J. Chem. Theory Comput. 4 (2008) pp. 435-447
  110. -------- -------- --- Thank You --- -------- --------
  111.  
  112.  
  113. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  114. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
  115. Berendsen
  116. GROMACS: Fast, Flexible and Free
  117. J. Comp. Chem. 26 (2005) pp. 1701-1719
  118. -------- -------- --- Thank You --- -------- --------
  119.  
  120.  
  121. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  122. E. Lindahl and B. Hess and D. van der Spoel
  123. GROMACS 3.0: A package for molecular simulation and trajectory analysis
  124. J. Mol. Mod. 7 (2001) pp. 306-317
  125. -------- -------- --- Thank You --- -------- --------
  126.  
  127.  
  128. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  129. H. J. C. Berendsen, D. van der Spoel and R. van Drunen
  130. GROMACS: A message-passing parallel molecular dynamics implementation
  131. Comp. Phys. Comm. 91 (1995) pp. 43-56
  132. -------- -------- --- Thank You --- -------- --------
  133.  
  134. Input Parameters:
  135. integrator = md
  136. tinit = 0
  137. dt = 0.002
  138. nsteps = 50000
  139. init-step = 0
  140. simulation-part = 1
  141. comm-mode = Linear
  142. nstcomm = 100
  143. bd-fric = 0
  144. ld-seed = -1283751987
  145. emtol = 10
  146. emstep = 0.01
  147. niter = 20
  148. fcstep = 0
  149. nstcgsteep = 1000
  150. nbfgscorr = 10
  151. rtpi = 0.05
  152. nstxout = 5000
  153. nstvout = 5000
  154. nstfout = 0
  155. nstlog = 5000
  156. nstcalcenergy = 100
  157. nstenergy = 5000
  158. nstxout-compressed = 5000
  159. compressed-x-precision = 1000
  160. cutoff-scheme = Verlet
  161. nstlist = 10
  162. ns-type = Grid
  163. pbc = xyz
  164. periodic-molecules = false
  165. verlet-buffer-tolerance = 0.005
  166. rlist = 1
  167. coulombtype = PME
  168. coulomb-modifier = Potential-shift
  169. rcoulomb-switch = 0
  170. rcoulomb = 1
  171. epsilon-r = 1
  172. epsilon-rf = inf
  173. vdw-type = Cut-off
  174. vdw-modifier = Potential-shift
  175. rvdw-switch = 0
  176. rvdw = 1
  177. DispCorr = EnerPres
  178. table-extension = 1
  179. fourierspacing = 0.16
  180. fourier-nx = 44
  181. fourier-ny = 44
  182. fourier-nz = 44
  183. pme-order = 4
  184. ewald-rtol = 1e-05
  185. ewald-rtol-lj = 0.001
  186. lj-pme-comb-rule = Geometric
  187. ewald-geometry = 0
  188. epsilon-surface = 0
  189. implicit-solvent = No
  190. gb-algorithm = Still
  191. nstgbradii = 1
  192. rgbradii = 1
  193. gb-epsilon-solvent = 80
  194. gb-saltconc = 0
  195. gb-obc-alpha = 1
  196. gb-obc-beta = 0.8
  197. gb-obc-gamma = 4.85
  198. gb-dielectric-offset = 0.009
  199. sa-algorithm = Ace-approximation
  200. sa-surface-tension = 2.05016
  201. tcoupl = V-rescale
  202. nsttcouple = 10
  203. nh-chain-length = 0
  204. print-nose-hoover-chain-variables = false
  205. pcoupl = Parrinello-Rahman
  206. pcoupltype = Isotropic
  207. nstpcouple = 10
  208. tau-p = 4
  209. compressibility (3x3):
  210. compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
  211. compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
  212. compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
  213. ref-p (3x3):
  214. ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
  215. ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
  216. ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
  217. refcoord-scaling = No
  218. posres-com (3):
  219. posres-com[0]= 0.00000e+00
  220. posres-com[1]= 0.00000e+00
  221. posres-com[2]= 0.00000e+00
  222. posres-comB (3):
  223. posres-comB[0]= 0.00000e+00
  224. posres-comB[1]= 0.00000e+00
  225. posres-comB[2]= 0.00000e+00
  226. QMMM = false
  227. QMconstraints = 0
  228. QMMMscheme = 0
  229. MMChargeScaleFactor = 1
  230. qm-opts:
  231. ngQM = 0
  232. constraint-algorithm = Lincs
  233. continuation = true
  234. Shake-SOR = false
  235. shake-tol = 0.0001
  236. lincs-order = 4
  237. lincs-iter = 1
  238. lincs-warnangle = 30
  239. nwall = 0
  240. wall-type = 9-3
  241. wall-r-linpot = -1
  242. wall-atomtype[0] = -1
  243. wall-atomtype[1] = -1
  244. wall-density[0] = 0
  245. wall-density[1] = 0
  246. wall-ewald-zfac = 3
  247. pull = false
  248. awh = false
  249. rotation = false
  250. interactiveMD = false
  251. disre = No
  252. disre-weighting = Conservative
  253. disre-mixed = false
  254. dr-fc = 1000
  255. dr-tau = 0
  256. nstdisreout = 100
  257. orire-fc = 0
  258. orire-tau = 0
  259. nstorireout = 100
  260. free-energy = no
  261. cos-acceleration = 0
  262. deform (3x3):
  263. deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  264. deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  265. deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
  266. simulated-tempering = false
  267. swapcoords = no
  268. userint1 = 0
  269. userint2 = 0
  270. userint3 = 0
  271. userint4 = 0
  272. userreal1 = 0
  273. userreal2 = 0
  274. userreal3 = 0
  275. userreal4 = 0
  276. applied-forces:
  277. electric-field:
  278. x:
  279. E0 = 0
  280. omega = 0
  281. t0 = 0
  282. sigma = 0
  283. y:
  284. E0 = 0
  285. omega = 0
  286. t0 = 0
  287. sigma = 0
  288. z:
  289. E0 = 0
  290. omega = 0
  291. t0 = 0
  292. sigma = 0
  293. grpopts:
  294. nrdf: 3895.83 63837.2
  295. ref-t: 300 300
  296. tau-t: 0.1 0.1
  297. annealing: No No
  298. annealing-npoints: 0 0
  299. acc: 0 0 0
  300. nfreeze: N N N
  301. energygrp-flags[ 0]: 0
  302.  
  303. Changing nstlist from 10 to 100, rlist from 1 to 1.167
  304.  
  305. Using 1 MPI thread
  306. Using 16 OpenMP threads
  307.  
  308. 1 GPU auto-selected for this run.
  309. Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
  310. PP:0,PME:0
  311.  
  312. NOTE: GROMACS was configured without NVML support hence it can not exploit
  313. application clocks of the detected Quadro M2000 GPU to improve performance.
  314. Recompile with the NVML library (compatible with the driver used) or set application clocks manually.
  315.  
  316. NOTE: GROMACS was configured without NVML support hence it can not exploit
  317. application clocks of the detected Quadro M2000 GPU to improve performance.
  318. Recompile with the NVML library (compatible with the driver used) or set application clocks manually.
  319.  
  320. Pinning threads with an auto-selected logical core stride of 1
  321. System total charge: -0.000
  322. Will do PME sum in reciprocal space for electrostatic interactions.
  323.  
  324. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  325. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
  326. A smooth particle mesh Ewald method
  327. J. Chem. Phys. 103 (1995) pp. 8577-8592
  328. -------- -------- --- Thank You --- -------- --------
  329.  
  330. Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
  331. Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
  332. Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073
  333.  
  334. Long Range LJ corr.: <C6> 3.1923e-04
  335. Generated table with 1083 data points for Ewald.
  336. Tabscale = 500 points/nm
  337. Generated table with 1083 data points for LJ6.
  338. Tabscale = 500 points/nm
  339. Generated table with 1083 data points for LJ12.
  340. Tabscale = 500 points/nm
  341. Generated table with 1083 data points for 1-4 COUL.
  342. Tabscale = 500 points/nm
  343. Generated table with 1083 data points for 1-4 LJ6.
  344. Tabscale = 500 points/nm
  345. Generated table with 1083 data points for 1-4 LJ12.
  346. Tabscale = 500 points/nm
  347.  
  348. Using GPU 8x8 nonbonded short-range kernels
  349.  
  350. Using a dual 8x4 pair-list setup updated with dynamic, rolling pruning:
  351. outer list: updated every 100 steps, buffer 0.167 nm, rlist 1.167 nm
  352. inner list: updated every 10 steps, buffer 0.002 nm, rlist 1.002 nm
  353. At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
  354. outer list: updated every 100 steps, buffer 0.319 nm, rlist 1.319 nm
  355. inner list: updated every 10 steps, buffer 0.043 nm, rlist 1.043 nm
  356.  
  357. Using geometric Lennard-Jones combination rule
  358.  
  359.  
  360. Initializing LINear Constraint Solver
  361.  
  362. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  363. B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
  364. LINCS: A Linear Constraint Solver for molecular simulations
  365. J. Comp. Chem. 18 (1997) pp. 1463-1472
  366. -------- -------- --- Thank You --- -------- --------
  367.  
  368. The number of constraints is 1984
  369.  
  370. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  371. S. Miyamoto and P. A. Kollman
  372. SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
  373. Water Models
  374. J. Comp. Chem. 13 (1992) pp. 952-962
  375. -------- -------- --- Thank You --- -------- --------
  376.  
  377.  
  378. Intra-simulation communication will occur every 10 steps.
  379. Center of mass motion removal mode is Linear
  380. We have the following groups for center of mass motion removal:
  381. 0: rest
  382.  
  383. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  384. G. Bussi, D. Donadio and M. Parrinello
  385. Canonical sampling through velocity rescaling
  386. J. Chem. Phys. 126 (2007) pp. 014101
  387. -------- -------- --- Thank You --- -------- --------
  388.  
  389. There are: 33876 Atoms
  390.  
  391. Started mdrun on rank 0 Wed Feb 28 19:23:24 2018
  392. Step Time
  393. 0 0.00000
  394.  
  395. Energies (kJ/mol)
  396. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  397. 3.93091e+03 2.23591e+02 1.86111e+03 2.95927e+03 7.96031e+03
  398. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  399. 9.30618e+04 -4.56887e+03 -6.35016e+05 2.98154e+03 -5.26606e+05
  400. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  401. 8.55246e+04 -4.41082e+05 -4.41062e+05 3.03729e+02 -2.26420e+02
  402. Pressure (bar) Constr. rmsd
  403. -1.93727e+02 3.02841e-05
  404.  
  405. step 200: timed with pme grid 44 44 44, coulomb cutoff 1.000: 1307.4 M-cycles
  406. step 400: timed with pme grid 40 40 40, coulomb cutoff 1.086: 1100.7 M-cycles
  407. step 600: timed with pme grid 36 36 36, coulomb cutoff 1.206: 1312.0 M-cycles
  408. step 800: timed with pme grid 40 40 40, coulomb cutoff 1.086: 1823.3 M-cycles
  409. step 1000: timed with pme grid 42 42 42, coulomb cutoff 1.034: 1084.8 M-cycles
  410. optimal pme grid 42 42 42, coulomb cutoff 1.034
  411. Step Time
  412. 5000 10.00000
  413.  
  414. Energies (kJ/mol)
  415. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  416. 3.81408e+03 2.51000e+02 1.81001e+03 2.96705e+03 7.97187e+03
  417. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  418. 9.40692e+04 -4.55248e+03 -6.35642e+05 2.55562e+03 -5.26756e+05
  419. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  420. 8.52103e+04 -4.41546e+05 -4.41190e+05 3.02613e+02 -2.24801e+02
  421. Pressure (bar) Constr. rmsd
  422. -4.12874e+01 2.88478e-05
  423.  
  424. Step Time
  425. 10000 20.00000
  426.  
  427. Energies (kJ/mol)
  428. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  429. 3.74535e+03 2.53348e+02 1.80359e+03 3.01105e+03 7.98561e+03
  430. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  431. 9.51157e+04 -4.58103e+03 -6.37033e+05 2.61371e+03 -5.27086e+05
  432. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  433. 8.38874e+04 -4.43198e+05 -4.41344e+05 2.97915e+02 -2.27625e+02
  434. Pressure (bar) Constr. rmsd
  435. 2.01994e+02 2.80778e-05
  436.  
  437. Step Time
  438. 15000 30.00000
  439.  
  440. Energies (kJ/mol)
  441. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  442. 3.79862e+03 2.59292e+02 1.90375e+03 3.03269e+03 7.96951e+03
  443. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  444. 9.41853e+04 -4.57276e+03 -6.35089e+05 2.62000e+03 -5.25892e+05
  445. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  446. 8.49289e+04 -4.40963e+05 -4.41500e+05 3.01614e+02 -2.26806e+02
  447. Pressure (bar) Constr. rmsd
  448. 1.95475e+02 2.73920e-05
  449.  
  450. Step Time
  451. 20000 40.00000
  452.  
  453. Energies (kJ/mol)
  454. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  455. 3.74591e+03 2.28070e+02 1.75276e+03 3.00774e+03 7.98380e+03
  456. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  457. 9.40194e+04 -4.55143e+03 -6.35599e+05 2.64141e+03 -5.26771e+05
  458. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  459. 8.43733e+04 -4.42398e+05 -4.41652e+05 2.99641e+02 -2.24697e+02
  460. Pressure (bar) Constr. rmsd
  461. -3.63672e+01 2.73290e-05
  462.  
  463. Step Time
  464. 25000 50.00000
  465.  
  466. Energies (kJ/mol)
  467. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  468. 3.80273e+03 2.54673e+02 1.92893e+03 3.02312e+03 8.02556e+03
  469. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  470. 9.46986e+04 -4.56388e+03 -6.36070e+05 2.63326e+03 -5.26267e+05
  471. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  472. 8.44835e+04 -4.41783e+05 -4.41807e+05 3.00032e+02 -2.25926e+02
  473. Pressure (bar) Constr. rmsd
  474. 5.20514e+01 2.84891e-05
  475.  
  476. Step Time
  477. 30000 60.00000
  478.  
  479. Energies (kJ/mol)
  480. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  481. 3.64308e+03 2.69114e+02 1.83624e+03 2.93642e+03 7.83512e+03
  482. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  483. 9.43847e+04 -4.59050e+03 -6.36923e+05 2.60790e+03 -5.28001e+05
  484. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  485. 8.40652e+04 -4.43935e+05 -4.41969e+05 2.98547e+02 -2.28567e+02
  486. Pressure (bar) Constr. rmsd
  487. 7.11596e+01 2.80504e-05
  488.  
  489. Step Time
  490. 35000 70.00000
  491.  
  492. Energies (kJ/mol)
  493. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  494. 3.87271e+03 2.44179e+02 1.80161e+03 2.99087e+03 7.94890e+03
  495. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  496. 9.32448e+04 -4.55680e+03 -6.34207e+05 2.60742e+03 -5.26053e+05
  497. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  498. 8.49437e+04 -4.41109e+05 -4.42120e+05 3.01666e+02 -2.25227e+02
  499. Pressure (bar) Constr. rmsd
  500. 5.37758e+01 2.68758e-05
  501.  
  502. Step Time
  503. 40000 80.00000
  504.  
  505. Energies (kJ/mol)
  506. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  507. 3.76080e+03 2.54442e+02 1.68395e+03 2.99437e+03 7.98869e+03
  508. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  509. 9.39502e+04 -4.55675e+03 -6.35655e+05 2.65420e+03 -5.26925e+05
  510. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  511. 8.38598e+04 -4.43065e+05 -4.42280e+05 2.97817e+02 -2.25222e+02
  512. Pressure (bar) Constr. rmsd
  513. -2.89238e+01 2.84841e-05
  514.  
  515. Step Time
  516. 45000 90.00000
  517.  
  518. Energies (kJ/mol)
  519. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  520. 3.80936e+03 2.40365e+02 1.84157e+03 3.05451e+03 7.98200e+03
  521. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  522. 9.32492e+04 -4.57017e+03 -6.33466e+05 2.58495e+03 -5.25274e+05
  523. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  524. 8.52468e+04 -4.40027e+05 -4.42441e+05 3.02742e+02 -2.26549e+02
  525. Pressure (bar) Constr. rmsd
  526. 1.18503e+02 2.59903e-05
  527.  
  528. Step Time
  529. 50000 100.00000
  530.  
  531. Writing checkpoint, step 50000 at Wed Feb 28 19:25:57 2018
  532.  
  533.  
  534. Energies (kJ/mol)
  535. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  536. 4.05700e+03 2.79840e+02 1.79805e+03 2.97583e+03 7.94072e+03
  537. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  538. 9.30207e+04 -4.57038e+03 -6.33621e+05 2.60657e+03 -5.25513e+05
  539. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  540. 8.53900e+04 -4.40123e+05 -4.42616e+05 3.03251e+02 -2.26570e+02
  541. Pressure (bar) Constr. rmsd
  542. -2.43613e+01 2.94082e-05
  543.  
  544. <====== ############### ==>
  545. <==== A V E R A G E S ====>
  546. <== ############### ======>
  547.  
  548. Statistics over 50001 steps using 501 frames
  549.  
  550. Energies (kJ/mol)
  551. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  552. 3.82827e+03 2.51703e+02 1.81002e+03 2.98604e+03 7.96516e+03
  553. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  554. 9.37059e+04 -4.56099e+03 -6.34690e+05 2.60131e+03 -5.26103e+05
  555. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  556. 8.44456e+04 -4.41657e+05 -4.41814e+05 2.99897e+02 -2.25642e+02
  557. Pressure (bar) Constr. rmsd
  558. 7.31157e+00 0.00000e+00
  559.  
  560. Box-X Box-Y Box-Z
  561. 6.95241e+00 6.95241e+00 6.95241e+00
  562.  
  563. Total Virial (kJ/mol)
  564. 2.81735e+04 2.20717e+01 5.10171e+00
  565. 2.23885e+01 2.80795e+04 5.39179e+01
  566. 4.22678e+00 5.37247e+01 2.79740e+04
  567.  
  568. Pressure (bar)
  569. -5.58816e-01 -2.01430e+00 -4.64558e-01
  570. -2.04569e+00 5.29394e+00 -5.85250e+00
  571. -3.78313e-01 -5.83325e+00 1.71996e+01
  572.  
  573. T-Protein T-non-Protein
  574. 2.99902e+02 2.99897e+02
  575.  
  576.  
  577. P P - P M E L O A D B A L A N C I N G
  578.  
  579. PP/PME load balancing changed the cut-off and PME settings:
  580. particle-particle PME
  581. rcoulomb rlist grid spacing 1/beta
  582. initial 1.000 nm 1.002 nm 44 44 44 0.158 nm 0.320 nm
  583. final 1.034 nm 1.036 nm 42 42 42 0.165 nm 0.331 nm
  584. cost-ratio 1.11 0.87
  585. (note that these numbers concern only part of the total PP and PME load)
  586.  
  587.  
  588. M E G A - F L O P S A C C O U N T I N G
  589.  
  590. NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
  591. RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
  592. W3=SPC/TIP3p W4=TIP4p (single or pairs)
  593. V&F=Potential and force V=Potential only F=Force only
  594.  
  595. Computing: M-Number M-Flops % Flops
  596. -----------------------------------------------------------------------------
  597. Pair Search distance check 1686.672592 15180.053 0.0
  598. NxN Ewald Elec. + LJ [F] 1745297.579520 115189640.248 98.1
  599. NxN Ewald Elec. + LJ [V&F] 17664.491264 1890100.565 1.6
  600. 1,4 nonbonded interactions 255.305106 22977.460 0.0
  601. Shift-X 16.971876 101.831 0.0
  602. Angles 177.353547 29795.396 0.0
  603. Propers 21.300426 4877.798 0.0
  604. RB-Dihedrals 197.503950 48783.476 0.0
  605. Virial 169.638921 3053.501 0.0
  606. Stop-CM 16.971876 169.719 0.0
  607. Calc-Ekin 338.827752 9148.349 0.0
  608. Lincs 99.201984 5952.119 0.0
  609. Lincs-Mat 2128.242564 8512.970 0.0
  610. Constraint-V 1793.835876 14350.687 0.0
  611. Constraint-Vir 169.493892 4067.853 0.0
  612. Settle 531.810636 171774.835 0.1
  613. -----------------------------------------------------------------------------
  614. Total 117418486.861 100.0
  615. -----------------------------------------------------------------------------
  616.  
  617.  
  618. R E A L C Y C L E A N D T I M E A C C O U N T I N G
  619.  
  620. On 1 MPI rank, each using 16 OpenMP threads
  621.  
  622. Computing: Num Num Call Wall time Giga-Cycles
  623. Ranks Threads Count (s) total sum %
  624. -----------------------------------------------------------------------------
  625. Neighbor search 1 16 501 0.985 59.244 0.6
  626. Launch GPU ops. 1 16 100002 4.723 284.115 3.1
  627. Force 1 16 50001 4.152 249.763 2.7
  628. Wait PME GPU gather 1 16 50001 25.177 1514.681 16.4
  629. Reduce GPU PME F 1 16 50001 7.821 470.510 5.1
  630. Wait GPU NB local 1 16 50001 83.009 4993.925 54.2
  631. NB X/F buffer ops. 1 16 99501 9.648 580.431 6.3
  632. Write traj. 1 16 11 0.202 12.158 0.1
  633. Update 1 16 50001 3.917 235.623 2.6
  634. Constraints 1 16 50001 7.526 452.791 4.9
  635. Rest 5.976 359.543 3.9
  636. -----------------------------------------------------------------------------
  637. Total 153.135 9212.785 100.0
  638. -----------------------------------------------------------------------------
  639.  
  640. Core t (s) Wall t (s) (%)
  641. Time: 2450.154 153.135 1600.0
  642. (ns/day) (hour/ns)
  643. Performance: 56.422 0.425
  644. Finished mdrun on rank 0 Wed Feb 28 19:25:57 2018
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