API tools faq
paste
Advertisement
mahmoodn

gromacs-lysozyme2

mahmoodn
Mar 1st, 2018
535
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 28.74 KB | None | 0 0
raw download clone embed print report
  1. Log file opened on Thu Mar 1 16:43:16 2018
  2. Host: orca pid: 16043 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 -pmefft cpu -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 Thu Mar 1 16:43:16 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 -4.41061e+05 3.03729e+02 -2.26420e+02
  402. Pressure (bar) Constr. rmsd
  403. -1.93714e+02 3.02841e-05
  404.  
  405. step 200: timed with pme grid 44 44 44, coulomb cutoff 1.000: 1089.4 M-cycles
  406. step 400: timed with pme grid 40 40 40, coulomb cutoff 1.086: 1748.7 M-cycles
  407. step 600: timed with pme grid 42 42 42, coulomb cutoff 1.034: 1043.3 M-cycles
  408. step 800: timed with pme grid 44 44 44, coulomb cutoff 1.000: 941.0 M-cycles
  409. step 1000: timed with pme grid 42 42 42, coulomb cutoff 1.034: 1051.1 M-cycles
  410. step 1200: timed with pme grid 44 44 44, coulomb cutoff 1.000: 914.5 M-cycles
  411. step 1400: timed with pme grid 44 44 44, coulomb cutoff 1.000: 927.0 M-cycles
  412. optimal pme grid 44 44 44, coulomb cutoff 1.000
  413. Step Time
  414. 5000 10.00000
  415.  
  416. Energies (kJ/mol)
  417. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  418. 3.74714e+03 2.29489e+02 1.85830e+03 2.98395e+03 7.97078e+03
  419. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  420. 9.35285e+04 -4.55650e+03 -6.34078e+05 2.97696e+03 -5.25339e+05
  421. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  422. 8.45352e+04 -4.40804e+05 -4.41210e+05 3.00215e+02 -2.25197e+02
  423. Pressure (bar) Constr. rmsd
  424. -2.00349e+01 2.88261e-05
  425.  
  426. Step Time
  427. 10000 20.00000
  428.  
  429. Energies (kJ/mol)
  430. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  431. 3.76239e+03 2.50806e+02 1.83982e+03 2.94719e+03 7.90688e+03
  432. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  433. 9.45513e+04 -4.55741e+03 -6.36591e+05 2.98575e+03 -5.26904e+05
  434. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  435. 8.36569e+04 -4.43247e+05 -4.41377e+05 2.97096e+02 -2.25287e+02
  436. Pressure (bar) Constr. rmsd
  437. 5.64360e+01 2.87589e-05
  438.  
  439. Step Time
  440. 15000 30.00000
  441.  
  442. Energies (kJ/mol)
  443. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  444. 3.83460e+03 2.16590e+02 1.84889e+03 2.99916e+03 7.93560e+03
  445. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  446. 9.28002e+04 -4.55083e+03 -6.33378e+05 2.99317e+03 -5.25300e+05
  447. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  448. 8.48697e+04 -4.40431e+05 -4.41563e+05 3.01403e+02 -2.24638e+02
  449. Pressure (bar) Constr. rmsd
  450. -1.74454e+02 2.86663e-05
  451.  
  452. Step Time
  453. 20000 40.00000
  454.  
  455. Energies (kJ/mol)
  456. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  457. 3.78986e+03 2.66748e+02 1.81543e+03 2.96847e+03 7.97993e+03
  458. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  459. 9.44517e+04 -4.56714e+03 -6.36137e+05 2.92373e+03 -5.26508e+05
  460. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  461. 8.35202e+04 -4.42988e+05 -4.41719e+05 2.96611e+02 -2.26249e+02
  462. Pressure (bar) Constr. rmsd
  463. 3.95898e+01 2.91447e-05
  464.  
  465. Step Time
  466. 25000 50.00000
  467.  
  468. Energies (kJ/mol)
  469. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  470. 3.83707e+03 2.48394e+02 1.76777e+03 2.94184e+03 7.93805e+03
  471. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  472. 9.35907e+04 -4.56210e+03 -6.35184e+05 2.86388e+03 -5.26559e+05
  473. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  474. 8.50755e+04 -4.41483e+05 -4.41893e+05 3.02134e+02 -2.25751e+02
  475. Pressure (bar) Constr. rmsd
  476. -9.14208e+01 2.99479e-05
  477.  
  478. Step Time
  479. 30000 60.00000
  480.  
  481. Energies (kJ/mol)
  482. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  483. 3.71125e+03 2.54892e+02 1.75736e+03 3.08602e+03 7.93436e+03
  484. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  485. 9.33267e+04 -4.55883e+03 -6.34928e+05 2.93775e+03 -5.26478e+05
  486. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  487. 8.34802e+04 -4.42998e+05 -4.42050e+05 2.96469e+02 -2.25427e+02
  488. Pressure (bar) Constr. rmsd
  489. -3.37393e+01 2.62942e-05
  490.  
  491. Step Time
  492. 35000 70.00000
  493.  
  494. Energies (kJ/mol)
  495. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  496. 3.82047e+03 2.20203e+02 1.80341e+03 2.93979e+03 7.98492e+03
  497. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  498. 9.40876e+04 -4.58164e+03 -6.34956e+05 2.97417e+03 -5.25708e+05
  499. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  500. 8.47481e+04 -4.40960e+05 -4.42229e+05 3.00972e+02 -2.27687e+02
  501. Pressure (bar) Constr. rmsd
  502. 1.52561e+02 2.76315e-05
  503.  
  504. Step Time
  505. 40000 80.00000
  506.  
  507. Energies (kJ/mol)
  508. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  509. 3.69603e+03 2.35419e+02 1.81726e+03 2.98399e+03 7.97008e+03
  510. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  511. 9.27449e+04 -4.55243e+03 -6.34747e+05 2.93503e+03 -5.26917e+05
  512. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  513. 8.38515e+04 -4.43065e+05 -4.42405e+05 2.97788e+02 -2.24795e+02
  514. Pressure (bar) Constr. rmsd
  515. -2.65799e+02 2.81826e-05
  516.  
  517. Step Time
  518. 45000 90.00000
  519.  
  520. Energies (kJ/mol)
  521. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  522. 3.98775e+03 2.76131e+02 1.79181e+03 3.00378e+03 7.85119e+03
  523. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  524. 9.39488e+04 -4.56189e+03 -6.33708e+05 2.96201e+03 -5.24449e+05
  525. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  526. 8.45410e+04 -4.39908e+05 -4.42578e+05 3.00236e+02 -2.25730e+02
  527. Pressure (bar) Constr. rmsd
  528. 2.53937e+02 2.58654e-05
  529.  
  530. Step Time
  531. 50000 100.00000
  532.  
  533. Writing checkpoint, step 50000 at Thu Mar 1 16:45:30 2018
  534.  
  535.  
  536. Energies (kJ/mol)
  537. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  538. 3.92206e+03 2.50274e+02 1.75320e+03 2.93181e+03 7.92636e+03
  539. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  540. 9.41958e+04 -4.56034e+03 -6.34365e+05 2.89714e+03 -5.25048e+05
  541. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  542. 8.45816e+04 -4.40467e+05 -4.42761e+05 3.00380e+02 -2.25576e+02
  543. Pressure (bar) Constr. rmsd
  544. 2.05125e+02 2.73693e-05
  545.  
  546. <====== ############### ==>
  547. <==== A V E R A G E S ====>
  548. <== ############### ======>
  549.  
  550. Statistics over 50001 steps using 501 frames
  551.  
  552. Energies (kJ/mol)
  553. Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
  554. 3.82581e+03 2.51064e+02 1.82695e+03 2.99284e+03 7.95823e+03
  555. LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
  556. 9.36774e+04 -4.55877e+03 -6.34876e+05 2.93589e+03 -5.25967e+05
  557. Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
  558. 8.44571e+04 -4.41510e+05 -4.41896e+05 2.99938e+02 -2.25423e+02
  559. Pressure (bar) Constr. rmsd
  560. 1.13389e+01 0.00000e+00
  561.  
  562. Box-X Box-Y Box-Z
  563. 6.95354e+00 6.95354e+00 6.95354e+00
  564.  
  565. Total Virial (kJ/mol)
  566. 2.79830e+04 4.10666e+01 1.94767e+01
  567. 4.08070e+01 2.81796e+04 -1.07072e+02
  568. 1.90603e+01 -1.07505e+02 2.79538e+04
  569.  
  570. Pressure (bar)
  571. 1.77313e+01 -4.13163e+00 -2.08938e+00
  572. -4.10589e+00 -3.07052e+00 8.96938e+00
  573. -2.04817e+00 9.01213e+00 1.93560e+01
  574.  
  575. T-Protein T-non-Protein
  576. 2.99828e+02 2.99945e+02
  577.  
  578.  
  579. M E G A - F L O P S A C C O U N T I N G
  580.  
  581. NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
  582. RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
  583. W3=SPC/TIP3p W4=TIP4p (single or pairs)
  584. V&F=Potential and force V=Potential only F=Force only
  585.  
  586. Computing: M-Number M-Flops % Flops
  587. -----------------------------------------------------------------------------
  588. Pair Search distance check 1627.620192 14648.582 0.0
  589. NxN Ewald Elec. + LJ [F] 1656800.487936 109348832.204 98.1
  590. NxN Ewald Elec. + LJ [V&F] 16768.815808 1794263.291 1.6
  591. 1,4 nonbonded interactions 255.305106 22977.460 0.0
  592. Shift-X 16.971876 101.831 0.0
  593. Angles 177.353547 29795.396 0.0
  594. Propers 21.300426 4877.798 0.0
  595. RB-Dihedrals 197.503950 48783.476 0.0
  596. Virial 169.638921 3053.501 0.0
  597. Stop-CM 16.971876 169.719 0.0
  598. Calc-Ekin 338.827752 9148.349 0.0
  599. Lincs 99.201984 5952.119 0.0
  600. Lincs-Mat 2128.242564 8512.970 0.0
  601. Constraint-V 1793.835876 14350.687 0.0
  602. Constraint-Vir 169.493892 4067.853 0.0
  603. Settle 531.810636 171774.835 0.2
  604. -----------------------------------------------------------------------------
  605. Total 111481310.071 100.0
  606. -----------------------------------------------------------------------------
  607.  
  608.  
  609. 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
  610.  
  611. On 1 MPI rank, each using 16 OpenMP threads
  612.  
  613. Computing: Num Num Call Wall time Giga-Cycles
  614. Ranks Threads Count (s) total sum %
  615. -----------------------------------------------------------------------------
  616. Neighbor search 1 16 501 0.976 56.194 0.7
  617. Launch GPU ops. 1 16 100002 2.967 170.895 2.2
  618. Force 1 16 50001 3.148 181.353 2.4
  619. Wait PME GPU spread 1 16 50001 16.858 971.061 12.6
  620. PME 3D-FFT 1 16 100002 11.167 643.229 8.4
  621. PME solve 1 16 50001 1.516 87.350 1.1
  622. Wait PME GPU gather 1 16 50001 5.972 343.978 4.5
  623. Reduce GPU PME F 1 16 50001 1.381 79.554 1.0
  624. Wait GPU NB local 1 16 50001 72.184 4157.986 54.0
  625. NB X/F buffer ops. 1 16 99501 6.505 374.684 4.9
  626. Write traj. 1 16 11 0.213 12.249 0.2
  627. Update 1 16 50001 2.358 135.846 1.8
  628. Constraints 1 16 50001 5.313 306.042 4.0
  629. Rest 3.127 180.147 2.3
  630. -----------------------------------------------------------------------------
  631. Total 133.684 7700.569 100.0
  632. -----------------------------------------------------------------------------
  633.  
  634. Core t (s) Wall t (s) (%)
  635. Time: 2138.940 133.684 1600.0
  636. (ns/day) (hour/ns)
  637. Performance: 64.631 0.371
  638. Finished mdrun on rank 0 Thu Mar 1 16:45:30 2018
Advertisement
Add Comment
Please, Sign In to add comment
Advertisement
Public Pastes
Advertisement
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy.  OK, I Understand
Not a member of Pastebin yet?
Sign Up, it unlocks many cool features!