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  1. Log file opened on Fri Mar 2 15:47:43 2018
  2. Host: orca pid: 14561 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 cpu -pme cpu -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 = 350012245
  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 = 2
  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 40, rlist from 1 to 1.096
  304.  
  305. Using 1 MPI thread
  306. Using 16 OpenMP threads
  307.  
  308. Pinning threads with an auto-selected logical core stride of 1
  309. System total charge: -0.000
  310. Will do PME sum in reciprocal space for electrostatic interactions.
  311.  
  312. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  313. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
  314. A smooth particle mesh Ewald method
  315. J. Chem. Phys. 103 (1995) pp. 8577-8592
  316. -------- -------- --- Thank You --- -------- --------
  317.  
  318. Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
  319. Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
  320. Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073
  321.  
  322. Long Range LJ corr.: <C6> 3.1923e-04
  323. Generated table with 1048 data points for Ewald.
  324. Tabscale = 500 points/nm
  325. Generated table with 1048 data points for LJ6.
  326. Tabscale = 500 points/nm
  327. Generated table with 1048 data points for LJ12.
  328. Tabscale = 500 points/nm
  329. Generated table with 1048 data points for 1-4 COUL.
  330. Tabscale = 500 points/nm
  331. Generated table with 1048 data points for 1-4 LJ6.
  332. Tabscale = 500 points/nm
  333. Generated table with 1048 data points for 1-4 LJ12.
  334. Tabscale = 500 points/nm
  335.  
  336. Using SIMD 4x4 nonbonded short-range kernels
  337.  
  338. Using a dual 4x4 pair-list setup updated with dynamic pruning:
  339. outer list: updated every 40 steps, buffer 0.096 nm, rlist 1.096 nm
  340. inner list: updated every 12 steps, buffer 0.003 nm, rlist 1.003 nm
  341. At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
  342. outer list: updated every 40 steps, buffer 0.211 nm, rlist 1.211 nm
  343. inner list: updated every 12 steps, buffer 0.048 nm, rlist 1.048 nm
  344.  
  345. Using geometric Lennard-Jones combination rule
  346.  
  347.  
  348. Initializing LINear Constraint Solver
  349.  
  350. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  351. B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
  352. LINCS: A Linear Constraint Solver for molecular simulations
  353. J. Comp. Chem. 18 (1997) pp. 1463-1472
  354. -------- -------- --- Thank You --- -------- --------
  355.  
  356. The number of constraints is 1984
  357.  
  358. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  359. S. Miyamoto and P. A. Kollman
  360. SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
  361. Water Models
  362. J. Comp. Chem. 13 (1992) pp. 952-962
  363. -------- -------- --- Thank You --- -------- --------
  364.  
  365.  
  366. Intra-simulation communication will occur every 10 steps.
  367. Center of mass motion removal mode is Linear
  368. We have the following groups for center of mass motion removal:
  369. 0: rest
  370.  
  371. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  372. G. Bussi, D. Donadio and M. Parrinello
  373. Canonical sampling through velocity rescaling
  374. J. Chem. Phys. 126 (2007) pp. 014101
  375. -------- -------- --- Thank You --- -------- --------
  376.  
  377. There are: 33876 Atoms
  378.  
  379. Started mdrun on rank 0 Fri Mar 2 15:47:43 2018
  380. Step Time
  381. 0 0.00000
  382.  
  383. Energies (kJ/mol)
  384. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  385. 3.93091e+03 2.23591e+02 1.86111e+03 2.95927e+03 7.96031e+03
  386. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  387. 9.30617e+04 -4.56887e+03 -6.35008e+05 2.98155e+03 -5.26598e+05
  388. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  389. 8.55246e+04 -4.41074e+05 -4.41054e+05 3.03729e+02 -2.26420e+02
  390. Pressure (bar) Constr. rmsd
  391. -1.93735e+02 3.02839e-05
  392.  
  393. Step Time
  394. 5000 10.00000
  395.  
  396. Energies (kJ/mol)
  397. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  398. 3.85896e+03 2.28569e+02 1.86876e+03 3.03576e+03 7.97678e+03
  399. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  400. 9.23450e+04 -4.55556e+03 -6.33417e+05 2.95125e+03 -5.25707e+05
  401. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  402. 8.46787e+04 -4.41029e+05 -4.41162e+05 3.00725e+02 -2.25105e+02
  403. Pressure (bar) Constr. rmsd
  404. -1.29163e+02 2.74567e-05
  405.  
  406. Step Time
  407. 10000 20.00000
  408.  
  409. Energies (kJ/mol)
  410. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  411. 3.81524e+03 2.39801e+02 1.77921e+03 2.93465e+03 7.95217e+03
  412. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  413. 9.40963e+04 -4.55762e+03 -6.35520e+05 3.07823e+03 -5.26182e+05
  414. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  415. 8.42839e+04 -4.41898e+05 -4.41311e+05 2.99323e+02 -2.25308e+02
  416. Pressure (bar) Constr. rmsd
  417. 3.62859e+01 2.86463e-05
  418.  
  419. Step Time
  420. 15000 30.00000
  421.  
  422. Energies (kJ/mol)
  423. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  424. 3.79639e+03 2.38328e+02 1.80826e+03 3.02907e+03 7.99581e+03
  425. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  426. 9.30922e+04 -4.55518e+03 -6.33821e+05 2.90283e+03 -5.25513e+05
  427. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  428. 8.51011e+04 -4.40412e+05 -4.41433e+05 3.02225e+02 -2.25067e+02
  429. Pressure (bar) Constr. rmsd
  430. -4.54185e+01 2.82589e-05
  431.  
  432. Step Time
  433. 20000 40.00000
  434.  
  435. Energies (kJ/mol)
  436. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  437. 3.68607e+03 2.33814e+02 1.83713e+03 3.12107e+03 8.05010e+03
  438. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  439. 9.47927e+04 -4.56521e+03 -6.36720e+05 2.86787e+03 -5.26696e+05
  440. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  441. 8.47600e+04 -4.41936e+05 -4.41540e+05 3.01014e+02 -2.26058e+02
  442. Pressure (bar) Constr. rmsd
  443. 1.88866e+02 2.64164e-05
  444.  
  445. Step Time
  446. 25000 50.00000
  447.  
  448. Energies (kJ/mol)
  449. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  450. 3.84497e+03 2.31316e+02 1.81174e+03 3.00274e+03 7.98610e+03
  451. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  452. 9.43887e+04 -4.56574e+03 -6.36830e+05 2.94152e+03 -5.27189e+05
  453. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  454. 8.36537e+04 -4.43535e+05 -4.41660e+05 2.97085e+02 -2.26110e+02
  455. Pressure (bar) Constr. rmsd
  456. 2.71759e+01 2.80783e-05
  457.  
  458. Step Time
  459. 30000 60.00000
  460.  
  461. Energies (kJ/mol)
  462. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  463. 3.85546e+03 2.39709e+02 1.83126e+03 2.88726e+03 7.92128e+03
  464. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  465. 9.48600e+04 -4.54785e+03 -6.36597e+05 2.93153e+03 -5.26619e+05
  466. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  467. 8.51241e+04 -4.41494e+05 -4.41800e+05 3.02307e+02 -2.24344e+02
  468. Pressure (bar) Constr. rmsd
  469. -9.14316e+00 3.02299e-05
  470.  
  471. Step Time
  472. 35000 70.00000
  473.  
  474. Energies (kJ/mol)
  475. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  476. 3.63275e+03 2.28526e+02 1.78491e+03 2.95363e+03 7.95967e+03
  477. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  478. 9.36332e+04 -4.55752e+03 -6.36108e+05 2.93222e+03 -5.27541e+05
  479. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  480. 8.32603e+04 -4.44280e+05 -4.41914e+05 2.95688e+02 -2.25298e+02
  481. Pressure (bar) Constr. rmsd
  482. -7.92795e+01 2.71188e-05
  483.  
  484. Step Time
  485. 40000 80.00000
  486.  
  487. Energies (kJ/mol)
  488. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  489. 3.85797e+03 2.64793e+02 1.86558e+03 2.94788e+03 7.96647e+03
  490. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  491. 9.38289e+04 -4.55687e+03 -6.35457e+05 2.83050e+03 -5.26451e+05
  492. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  493. 8.52091e+04 -4.41242e+05 -4.42033e+05 3.02609e+02 -2.25234e+02
  494. Pressure (bar) Constr. rmsd
  495. -1.69388e+01 2.91565e-05
  496.  
  497. Step Time
  498. 45000 90.00000
  499.  
  500. Energies (kJ/mol)
  501. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  502. 3.78822e+03 2.20884e+02 1.73361e+03 2.93057e+03 8.00415e+03
  503. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  504. 9.33730e+04 -4.55638e+03 -6.34932e+05 2.91973e+03 -5.26518e+05
  505. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  506. 8.38725e+04 -4.42645e+05 -4.42162e+05 2.97862e+02 -2.25185e+02
  507. Pressure (bar) Constr. rmsd
  508. -1.29659e+02 2.83754e-05
  509.  
  510. Step Time
  511. 50000 100.00000
  512.  
  513. Writing checkpoint, step 50000 at Fri Mar 2 15:53:23 2018
  514.  
  515.  
  516. Energies (kJ/mol)
  517. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  518. 3.70632e+03 2.38879e+02 1.82614e+03 2.99008e+03 7.89146e+03
  519. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  520. 9.29397e+04 -4.56180e+03 -6.35183e+05 2.87004e+03 -5.27283e+05
  521. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  522. 8.44466e+04 -4.42836e+05 -4.42283e+05 2.99901e+02 -2.25721e+02
  523. Pressure (bar) Constr. rmsd
  524. -5.33410e+01 2.69359e-05
  525.  
  526. <====== ############### ==>
  527. <==== A V E R A G E S ====>
  528. <== ############### ======>
  529.  
  530. Statistics over 50001 steps using 501 frames
  531.  
  532. Energies (kJ/mol)
  533. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  534. 3.81615e+03 2.47853e+02 1.82775e+03 2.99103e+03 7.96759e+03
  535. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  536. 9.36933e+04 -4.56189e+03 -6.35027e+05 2.93405e+03 -5.26111e+05
  537. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  538. 8.44357e+04 -4.41675e+05 -4.41666e+05 2.99862e+02 -2.25731e+02
  539. Pressure (bar) Constr. rmsd
  540. 1.53676e+01 0.00000e+00
  541.  
  542. Box-X Box-Y Box-Z
  543. 6.95196e+00 6.95196e+00 6.95196e+00
  544.  
  545. Total Virial (kJ/mol)
  546. 2.79890e+04 4.08265e+01 -5.63704e+01
  547. 4.01560e+01 2.81213e+04 -4.48169e+01
  548. -5.66951e+01 -4.43083e+01 2.78643e+04
  549.  
  550. Pressure (bar)
  551. 1.52160e+01 -3.98532e+00 3.85860e+00
  552. -3.91914e+00 5.34359e+00 2.76083e+00
  553. 3.89069e+00 2.71055e+00 2.55431e+01
  554.  
  555. T-Protein T-non-Protein
  556. 3.00051e+02 2.99851e+02
  557.  
  558.  
  559. M E G A - F L O P S A C C O U N T I N G
  560.  
  561. NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
  562. RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
  563. W3=SPC/TIP3p W4=TIP4p (single or pairs)
  564. V&F=Potential and force V=Potential only F=Force only
  565.  
  566. Computing: M-Number M-Flops % Flops
  567. -----------------------------------------------------------------------------
  568. Pair Search distance check 14085.486140 126769.375 0.4
  569. NxN QSTab Elec. + LJ [F] 433081.733096 17756351.057 52.5
  570. NxN QSTab Elec. + LJ [V&F] 4383.435480 258622.693 0.8
  571. NxN QSTab Elec. [F] 383528.973736 13039985.107 38.5
  572. NxN QSTab Elec. [V&F] 3881.382408 159136.679 0.5
  573. 1,4 nonbonded interactions 255.305106 22977.460 0.1
  574. Calc Weights 5081.501628 182934.059 0.5
  575. Spread Q Bspline 108405.368064 216810.736 0.6
  576. Gather F Bspline 108405.368064 650432.208 1.9
  577. 3D-FFT 139519.590336 1116156.723 3.3
  578. Solve PME 96.801936 6195.324 0.0
  579. Shift-X 42.378876 254.273 0.0
  580. Angles 177.353547 29795.396 0.1
  581. Propers 21.300426 4877.798 0.0
  582. RB-Dihedrals 197.503950 48783.476 0.1
  583. Virial 169.638921 3053.501 0.0
  584. Stop-CM 16.971876 169.719 0.0
  585. Calc-Ekin 338.827752 9148.349 0.0
  586. Lincs 99.201984 5952.119 0.0
  587. Lincs-Mat 2128.242564 8512.970 0.0
  588. Constraint-V 1793.835876 14350.687 0.0
  589. Constraint-Vir 169.493892 4067.853 0.0
  590. Settle 531.810636 171774.835 0.5
  591. -----------------------------------------------------------------------------
  592. Total 33837112.397 100.0
  593. -----------------------------------------------------------------------------
  594.  
  595.  
  596. 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
  597.  
  598. On 1 MPI rank, each using 16 OpenMP threads
  599.  
  600. Computing: Num Num Call Wall time Giga-Cycles
  601. Ranks Threads Count (s) total sum %
  602. -----------------------------------------------------------------------------
  603. Neighbor search 1 16 1251 7.434 428.184 2.2
  604. Force 1 16 50001 227.011 13075.826 66.8
  605. PME mesh 1 16 50001 58.587 3374.593 17.2
  606. NB X/F buffer ops. 1 16 98751 28.296 1629.843 8.3
  607. Write traj. 1 16 11 0.231 13.319 0.1
  608. Update 1 16 50001 6.057 348.881 1.8
  609. Constraints 1 16 50001 10.211 588.178 3.0
  610. Rest 2.042 117.592 0.6
  611. -----------------------------------------------------------------------------
  612. Total 339.868 19576.415 100.0
  613. -----------------------------------------------------------------------------
  614. Breakdown of PME mesh computation
  615. -----------------------------------------------------------------------------
  616. PME spread 1 16 50001 26.431 1522.424 7.8
  617. PME gather 1 16 50001 15.737 906.428 4.6
  618. PME 3D-FFT 1 16 100002 14.328 825.270 4.2
  619. PME solve Elec 1 16 50001 0.963 55.494 0.3
  620. -----------------------------------------------------------------------------
  621.  
  622. Core t (s) Wall t (s) (%)
  623. Time: 5437.892 339.868 1600.0
  624. (ns/day) (hour/ns)
  625. Performance: 25.422 0.944
  626. Finished mdrun on rank 0 Fri Mar 2 15:53:23 2018
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