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- :-) GROMACS - gmx mdrun, 2021.2 (-:
- GROMACS is written by:
- Andrey Alekseenko Emile Apol Rossen Apostolov
- Paul Bauer Herman J.C. Berendsen Par Bjelkmar
- Christian Blau Viacheslav Bolnykh Kevin Boyd
- Aldert van Buuren Rudi van Drunen Anton Feenstra
- Gilles Gouaillardet Alan Gray Gerrit Groenhof
- Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
- Aleksei Iupinov Christoph Junghans Joe Jordan
- Dimitrios Karkoulis Peter Kasson Jiri Kraus
- Carsten Kutzner Per Larsson Justin A. Lemkul
- Viveca Lindahl Magnus Lundborg Erik Marklund
- Pascal Merz Pieter Meulenhoff Teemu Murtola
- Szilard Pall Sander Pronk Roland Schulz
- Michael Shirts Alexey Shvetsov Alfons Sijbers
- Peter Tieleman Jon Vincent Teemu Virolainen
- Christian Wennberg Maarten Wolf Artem Zhmurov
- and the project leaders:
- Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
- Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- Copyright (c) 2001-2019, The GROMACS development team at
- Uppsala University, Stockholm University and
- the Royal Institute of Technology, Sweden.
- check out http://www.gromacs.org for more information.
- GROMACS is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License
- as published by the Free Software Foundation; either version 2.1
- of the License, or (at your option) any later version.
- GROMACS: gmx mdrun, version 2021.2
- Executable: /mnt/ssd0/sclapps/gromacs20212g/bin/gmx_mpi
- Data prefix: /mnt/ssd0/sclapps/gromacs20212g
- Working dir: /mnt/ssd0/sharedjobfolder/adighe6/gromacswork/2.5
- Process ID: 36774
- Command line:
- gmx_mpi -quiet -copyright mdrun -s nvt_ions.tpr -deffnm nvt_ions1 -v -ntomp 4 -dlb yes -notunepme
- GROMACS version: 2021.2
- Verified release checksum is d91a739522d82c53dc47c2276b9ac5fae3b2119283e84e3a1c7bed8ce741fda2
- Precision: mixed
- Memory model: 64 bit
- MPI library: MPI
- OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
- GPU support: disabled
- SIMD instructions: AVX2_256
- FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
- RDTSCP usage: enabled
- TNG support: enabled
- Hwloc support: disabled
- Tracing support: disabled
- C compiler: /usr/bin/gcc GNU 8.3.0
- C compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
- C++ compiler: /usr/bin/g++ GNU 8.3.0
- C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
- Running on 2 nodes with total 64 cores, 128 logical cores
- Cores per node: 32
- Logical cores per node: 64
- Hardware detected on host maselnode1.che.uic.edu (the node of MPI rank 0):
- CPU info:
- Vendor: Intel
- Brand: Intel(R) Xeon(R) CPU E5-2683 v4 @ 2.10GHz
- Family: 6 Model: 79 Stepping: 1
- Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
- Hardware topology: Basic
- Sockets, cores, and logical processors:
- Socket 0: [ 0 32] [ 1 33] [ 2 34] [ 3 35] [ 4 36] [ 5 37] [ 6 38] [ 7 39] [ 8 40] [ 9 41] [ 10 42] [ 11 43] [ 12 44] [ 13 45] [ 14 46] [ 15 47]
- Socket 1: [ 16 48] [ 17 49] [ 18 50] [ 19 51] [ 20 52] [ 21 53] [ 22 54] [ 23 55] [ 24 56] [ 25 57] [ 26 58] [ 27 59] [ 28 60] [ 29 61] [ 30 62] [ 31 63]
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
- Lindahl
- GROMACS: High performance molecular simulations through multi-level
- parallelism from laptops to supercomputers
- SoftwareX 1 (2015) pp. 19-25
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
- Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
- GROMACS
- In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
- Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
- GROMACS 4.5: a high-throughput and highly parallel open source molecular
- simulation toolkit
- Bioinformatics 29 (2013) pp. 845-54
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
- GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
- molecular simulation
- J. Chem. Theory Comput. 4 (2008) pp. 435-447
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
- Berendsen
- GROMACS: Fast, Flexible and Free
- J. Comp. Chem. 26 (2005) pp. 1701-1719
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- E. Lindahl and B. Hess and D. van der Spoel
- GROMACS 3.0: A package for molecular simulation and trajectory analysis
- J. Mol. Mod. 7 (2001) pp. 306-317
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- H. J. C. Berendsen, D. van der Spoel and R. van Drunen
- GROMACS: A message-passing parallel molecular dynamics implementation
- Comp. Phys. Comm. 91 (1995) pp. 43-56
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
- https://doi.org/10.5281/zenodo.4723562
- -------- -------- --- Thank You --- -------- --------
- Input Parameters:
- integrator = md
- tinit = 0
- dt = 0.002
- nsteps = 500000
- init-step = 0
- simulation-part = 1
- mts = false
- comm-mode = Linear
- nstcomm = 10000
- bd-fric = 0
- ld-seed = -137980177
- emtol = 10
- emstep = 0.01
- niter = 20
- fcstep = 0
- nstcgsteep = 1000
- nbfgscorr = 10
- rtpi = 0.05
- nstxout = 10000
- nstvout = 10000
- nstfout = 0
- nstlog = 10000
- nstcalcenergy = 10000
- nstenergy = 10000
- nstxout-compressed = 0
- compressed-x-precision = 1000
- cutoff-scheme = Verlet
- nstlist = 40
- pbc = xyz
- periodic-molecules = false
- verlet-buffer-tolerance = 5e-05
- rlist = 1.3
- coulombtype = PME
- coulomb-modifier = Potential-shift
- rcoulomb-switch = 0
- rcoulomb = 1
- epsilon-r = 1
- epsilon-rf = inf
- vdw-type = Cut-off
- vdw-modifier = Potential-shift
- rvdw-switch = 0
- rvdw = 1
- DispCorr = EnerPres
- table-extension = 1
- fourierspacing = 0.16
- fourier-nx = 44
- fourier-ny = 44
- fourier-nz = 44
- pme-order = 4
- ewald-rtol = 1e-05
- ewald-rtol-lj = 0.001
- lj-pme-comb-rule = Geometric
- ewald-geometry = 0
- epsilon-surface = 0
- tcoupl = V-rescale
- nsttcouple = 10
- nh-chain-length = 0
- print-nose-hoover-chain-variables = false
- pcoupl = No
- pcoupltype = Isotropic
- nstpcouple = -1
- tau-p = 1
- compressibility (3x3):
- compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
- compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
- compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
- ref-p (3x3):
- ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
- ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
- ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
- refcoord-scaling = No
- posres-com (3):
- posres-com[0]= 0.00000e+00
- posres-com[1]= 0.00000e+00
- posres-com[2]= 0.00000e+00
- posres-comB (3):
- posres-comB[0]= 0.00000e+00
- posres-comB[1]= 0.00000e+00
- posres-comB[2]= 0.00000e+00
- QMMM = false
- qm-opts:
- ngQM = 0
- constraint-algorithm = Lincs
- continuation = false
- Shake-SOR = false
- shake-tol = 0.0001
- lincs-order = 4
- lincs-iter = 2
- lincs-warnangle = 30
- nwall = 0
- wall-type = 9-3
- wall-r-linpot = -1
- wall-atomtype[0] = -1
- wall-atomtype[1] = -1
- wall-density[0] = 0
- wall-density[1] = 0
- wall-ewald-zfac = 3
- pull = false
- awh = false
- rotation = false
- interactiveMD = false
- disre = No
- disre-weighting = Conservative
- disre-mixed = false
- dr-fc = 1000
- dr-tau = 0
- nstdisreout = 100
- orire-fc = 0
- orire-tau = 0
- nstorireout = 100
- free-energy = no
- cos-acceleration = 0
- deform (3x3):
- deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
- deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
- deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
- simulated-tempering = false
- swapcoords = no
- userint1 = 0
- userint2 = 0
- userint3 = 0
- userint4 = 0
- userreal1 = 0
- userreal2 = 0
- userreal3 = 0
- userreal4 = 0
- applied-forces:
- electric-field:
- x:
- E0 = 0
- omega = 0
- t0 = 0
- sigma = 0
- y:
- E0 = 0
- omega = 0
- t0 = 0
- sigma = 0
- z:
- E0 = 0
- omega = 0
- t0 = 0
- sigma = 0
- density-guided-simulation:
- active = false
- group = protein
- similarity-measure = inner-product
- atom-spreading-weight = unity
- force-constant = 1e+09
- gaussian-transform-spreading-width = 0.2
- gaussian-transform-spreading-range-in-multiples-of-width = 4
- reference-density-filename = reference.mrc
- nst = 1
- normalize-densities = true
- adaptive-force-scaling = false
- adaptive-force-scaling-time-constant = 4
- shift-vector =
- transformation-matrix =
- grpopts:
- nrdf: 959.931 40659.1
- ref-t: 300 300
- tau-t: 0.1 0.1
- annealing: No No
- annealing-npoints: 0 0
- acc: 0 0 0
- nfreeze: N N N
- energygrp-flags[ 0]: 0
- Initializing Domain Decomposition on 32 ranks
- Dynamic load balancing: on
- Using update groups, nr 7107, average size 2.9 atoms, max. radius 0.099 nm
- Minimum cell size due to atom displacement: 0.334 nm
- Initial maximum distances in bonded interactions:
- two-body bonded interactions: 0.397 nm, LJ-14, atoms 138 146
- multi-body bonded interactions: 0.397 nm, Ryckaert-Bell., atoms 138 146
- Minimum cell size due to bonded interactions: 0.437 nm
- Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
- Guess for relative PME load: 0.15
- Will use 24 particle-particle and 8 PME only ranks
- This is a guess, check the performance at the end of the log file
- Using 8 separate PME ranks, as guessed by mdrun
- Optimizing the DD grid for 24 cells with a minimum initial size of 0.546 nm
- The maximum allowed number of cells is: X 10 Y 10 Z 8
- Domain decomposition grid 4 x 6 x 1, separate PME ranks 8
- PME domain decomposition: 4 x 2 x 1
- Interleaving PP and PME ranks
- This rank does only particle-particle work.
- Domain decomposition rank 0, coordinates 0 0 0
- The maximum number of communication pulses is: X 3 Y 3
- The minimum size for domain decomposition cells is 0.677 nm
- The requested allowed shrink of DD cells (option -dds) is: 0.80
- The allowed shrink of domain decomposition cells is: X 0.49 Y 0.74
- The maximum allowed distance for atom groups involved in interactions is:
- non-bonded interactions 1.498 nm
- two-body bonded interactions (-rdd) 1.498 nm
- multi-body bonded interactions (-rdd) 0.677 nm
- Using two step summing over 2 groups of on average 12.0 ranks
- Using 32 MPI processes
- Non-default thread affinity set, disabling internal thread affinity
- Using 4 OpenMP threads per MPI process
- System total charge: -0.000
- Will do PME sum in reciprocal space for electrostatic interactions.
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
- A smooth particle mesh Ewald method
- J. Chem. Phys. 103 (1995) pp. 8577-8592
- -------- -------- --- Thank You --- -------- --------
- Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
- Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
- Initialized non-bonded Ewald tables, spacing: 9.33e-04 size: 1073
- Generated table with 1150 data points for 1-4 COUL.
- Tabscale = 500 points/nm
- Generated table with 1150 data points for 1-4 LJ6.
- Tabscale = 500 points/nm
- Generated table with 1150 data points for 1-4 LJ12.
- Tabscale = 500 points/nm
- Long Range LJ corr.: <C6> 3.2041e-04
- Using SIMD 4x8 nonbonded short-range kernels
- Using a dual 4x8 pair-list setup updated with dynamic pruning:
- outer list: updated every 40 steps, buffer 0.300 nm, rlist 1.300 nm
- inner list: updated every 4 steps, buffer 0.016 nm, rlist 1.016 nm
- At tolerance 5e-05 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
- outer list: updated every 40 steps, buffer 0.391 nm, rlist 1.391 nm
- inner list: updated every 4 steps, buffer 0.025 nm, rlist 1.025 nm
- Using geometric Lennard-Jones combination rule
- Removing pbc first time
- Initializing LINear Constraint Solver
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
- LINCS: A Linear Constraint Solver for molecular simulations
- J. Comp. Chem. 18 (1997) pp. 1463-1472
- -------- -------- --- Thank You --- -------- --------
- The number of constraints is 180
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- S. Miyamoto and P. A. Kollman
- SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
- Water Models
- J. Comp. Chem. 13 (1992) pp. 952-962
- -------- -------- --- Thank You --- -------- --------
- Linking all bonded interactions to atoms
- Intra-simulation communication will occur every 10 steps.
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- G. Bussi, D. Donadio and M. Parrinello
- Canonical sampling through velocity rescaling
- J. Chem. Phys. 126 (2007) pp. 014101
- -------- -------- --- Thank You --- -------- --------
- There are: 20581 Atoms
- Atom distribution over 24 domains: av 857 stddev 34 min 833 max 883
- Constraining the starting coordinates (step 0)
- Constraining the coordinates at t0-dt (step 0)
- Center of mass motion removal mode is Linear
- We have the following groups for center of mass motion removal:
- 0: rest
- RMS relative constraint deviation after constraining: 1.03e-07
- Initial temperature: 300.491 K
- Started mdrun on rank 0 Sat Jun 5 19:24:37 2021
- Step Time
- 0 0.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 1.95655e+01 3.26847e+02 1.73961e+01 5.04810e+02 3.17094e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.30093e+03 8.07876e+04 -2.62275e+03 -5.66376e+05 2.89486e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.78829e+05 5.19958e+04 -4.26833e+05 -4.26833e+05 3.00520e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -3.43997e+03 1.30522e-06
- DD step 39 vol min/aver 1.000 load imb.: force 11.1% pme mesh/force 2.665
- DD step 9999 vol min/aver 0.837 load imb.: force 6.6% pme mesh/force 1.621
- Step Time
- 10000 20.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.64898e+02 8.40585e+02 5.09667e+01 1.42320e+02 2.61013e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.09051e+03 6.62806e+04 -2.62275e+03 -4.95883e+05 2.69592e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22879e+05 5.24227e+04 -3.70456e+05 -4.26386e+05 3.02986e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -8.51684e+02 1.23345e-06
- DD load balancing is limited by minimum cell size in dimension Y
- DD step 19999 vol min/aver 0.825! load imb.: force 5.4% pme mesh/force 1.761
- Step Time
- 20000 40.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.92989e+02 8.09229e+02 7.80418e+01 1.24286e+02 2.72045e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.09472e+03 6.41306e+04 -2.62275e+03 -4.93400e+05 2.64909e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22572e+05 5.21806e+04 -3.70391e+05 -4.26372e+05 3.01587e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.33877e+03 1.36070e-06
- DD step 29999 vol min/aver 0.802 load imb.: force 4.0% pme mesh/force 1.608
- Step Time
- 30000 60.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.22638e+02 8.37206e+02 8.34757e+01 6.33412e+01 2.42656e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.04424e+03 6.54795e+04 -2.62275e+03 -4.94920e+05 2.54454e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23025e+05 5.19198e+04 -3.71105e+05 -4.26388e+05 3.00080e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.02925e+03 1.20095e-06
- DD load balancing is limited by minimum cell size in dimension Y
- DD step 39999 vol min/aver 0.832! load imb.: force 5.7% pme mesh/force 1.594
- Step Time
- 40000 80.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.45272e+02 8.13773e+02 6.24154e+01 1.99516e+01 2.55178e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.05460e+03 6.50580e+04 -2.62275e+03 -4.94366e+05 2.64879e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22830e+05 5.17409e+04 -3.71090e+05 -4.26368e+05 2.99046e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.21752e+03 1.16517e-06
- DD step 49999 vol min/aver 0.853 load imb.: force 7.9% pme mesh/force 1.674
- Step Time
- 50000 100.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.78245e+02 8.56713e+02 5.83726e+01 6.65521e+01 2.68607e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.08565e+03 6.44310e+04 -2.62275e+03 -4.92054e+05 2.62162e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.21010e+05 5.21594e+04 -3.68851e+05 -4.26370e+05 3.01465e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.09785e+03 1.26677e-06
- DD step 59999 vol min/aver 0.864 load imb.: force 4.3% pme mesh/force 1.751
- Step Time
- 60000 120.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.25468e+02 7.69561e+02 5.78308e+01 9.73209e+01 2.53792e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.12195e+03 6.48014e+04 -2.62275e+03 -4.94054e+05 2.60957e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22740e+05 5.18739e+04 -3.70866e+05 -4.26368e+05 2.99815e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.13644e+03 1.12578e-06
- DD step 69999 vol min/aver 0.758 load imb.: force 3.1% pme mesh/force 1.669
- Step Time
- 70000 140.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.61310e+02 9.18715e+02 3.86484e+01 3.22319e+01 2.73798e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.07610e+03 6.49040e+04 -2.62275e+03 -4.93433e+05 2.50169e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22049e+05 5.19202e+04 -3.70129e+05 -4.26368e+05 3.00082e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.01690e+03 1.10510e-06
- DD step 79999 vol min/aver 0.798 load imb.: force 4.6% pme mesh/force 1.515
- Step Time
- 80000 160.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.86565e+02 8.72055e+02 4.60017e+01 5.86514e+01 2.62847e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.09733e+03 6.56432e+04 -2.62275e+03 -4.94590e+05 2.61423e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22331e+05 5.21626e+04 -3.70169e+05 -4.26367e+05 3.01483e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -9.41200e+02 1.26554e-06
- DD load balancing is limited by minimum cell size in dimension Y
- DD step 89999 vol min/aver 0.816! load imb.: force 10.9% pme mesh/force 1.574
- Step Time
- 90000 180.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.48619e+02 9.19157e+02 6.11105e+01 4.37963e+01 2.93758e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.11297e+03 6.58220e+04 -2.62275e+03 -4.94860e+05 2.47177e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22509e+05 5.19916e+04 -3.70518e+05 -4.26365e+05 3.00495e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -8.90271e+02 1.29238e-06
- DD step 99999 vol min/aver 0.828 load imb.: force 7.0% pme mesh/force 1.599
- Step Time
- 100000 200.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.44718e+02 7.78863e+02 4.22625e+01 7.44081e+01 2.36271e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.07329e+03 6.65722e+04 -2.62275e+03 -4.95866e+05 2.53997e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22927e+05 5.12104e+04 -3.71716e+05 -4.26366e+05 2.95980e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -7.80831e+02 1.13195e-06
- DD step 109999 vol min/aver 0.879 load imb.: force 6.8% pme mesh/force 1.613
- Step Time
- 110000 220.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.54183e+02 8.09131e+02 4.92883e+01 5.32089e+01 2.51968e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.05652e+03 6.56500e+04 -2.62275e+03 -4.95104e+05 2.53316e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23069e+05 5.19348e+04 -3.71134e+05 -4.26370e+05 3.00166e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -9.53641e+02 1.20531e-06
- DD step 119999 vol min/aver 0.852 load imb.: force 6.8% pme mesh/force 1.509
- Step Time
- 120000 240.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.39608e+02 9.84292e+02 6.49301e+01 -1.08262e+01 2.46035e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.08693e+03 6.56647e+04 -2.62275e+03 -4.93973e+05 2.59023e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.21730e+05 5.14708e+04 -3.70259e+05 -4.26375e+05 2.97485e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -9.29986e+02 1.16434e-06
- DD step 129999 vol min/aver 0.804 load imb.: force 4.3% pme mesh/force 1.487
- Step Time
- 130000 260.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.36330e+02 8.28626e+02 5.00063e+01 1.52039e+01 2.39154e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.05430e+03 6.60570e+04 -2.62275e+03 -4.95091e+05 2.62321e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22609e+05 5.18162e+04 -3.70793e+05 -4.26358e+05 2.99482e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -9.51810e+02 1.23614e-06
- DD step 139999 vol min/aver 0.780 load imb.: force 4.6% pme mesh/force 1.454
- Step Time
- 140000 280.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.47451e+02 8.55478e+02 3.91970e+01 3.33786e+01 2.88807e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.15802e+03 6.66215e+04 -2.62275e+03 -4.95196e+05 2.53802e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22037e+05 5.17571e+04 -3.70280e+05 -4.26343e+05 2.99140e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -6.99858e+02 1.39802e-06
- DD step 149999 vol min/aver 0.774 load imb.: force 4.3% pme mesh/force 1.643
- Step Time
- 150000 300.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.17281e+02 9.18972e+02 6.07919e+01 1.05047e+00 2.39842e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.08792e+03 6.52469e+04 -2.62275e+03 -4.94923e+05 2.61168e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23161e+05 5.17397e+04 -3.71422e+05 -4.26346e+05 2.99039e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.17989e+03 1.36533e-06
- DD step 159999 vol min/aver 0.811 load imb.: force 5.4% pme mesh/force 1.437
- Step Time
- 160000 320.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 1.94578e+02 8.86347e+02 5.79546e+01 -1.84695e+01 2.62664e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.07059e+03 6.54296e+04 -2.62275e+03 -4.95304e+05 2.56860e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23475e+05 5.11976e+04 -3.72278e+05 -4.26356e+05 2.95906e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.01834e+03 1.26298e-06
- DD step 169999 vol min/aver 0.820 load imb.: force 7.3% pme mesh/force 1.766
- Step Time
- 170000 340.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.61597e+02 8.28217e+02 5.45751e+01 8.91896e+00 2.70009e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.02226e+03 6.58329e+04 -2.62275e+03 -4.95391e+05 2.54127e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23194e+05 5.22168e+04 -3.70978e+05 -4.26353e+05 3.01796e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.02035e+03 1.11424e-06
- DD step 179999 vol min/aver 0.777 load imb.: force 4.9% pme mesh/force 1.589
- Step Time
- 180000 360.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.15188e+02 8.68529e+02 6.12402e+01 5.41956e+01 2.77409e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.10169e+03 6.65507e+04 -2.62275e+03 -4.95866e+05 2.50393e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22856e+05 5.27884e+04 -3.70067e+05 -4.26352e+05 3.05100e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -7.20779e+02 1.37731e-06
- DD step 189999 vol min/aver 0.818 load imb.: force 6.3% pme mesh/force 1.634
- Step Time
- 190000 380.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.21288e+02 7.52477e+02 4.94282e+01 3.51291e+01 2.48931e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.01166e+03 6.64227e+04 -2.62275e+03 -4.96728e+05 2.48088e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.24129e+05 5.11619e+04 -3.72967e+05 -4.26355e+05 2.95700e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -9.46375e+02 1.23046e-06
- DD step 199999 vol min/aver 0.837 load imb.: force 3.6% pme mesh/force 1.626
- Step Time
- 200000 400.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 3.36209e+02 9.39935e+02 5.84881e+01 6.48977e+01 3.27417e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.18080e+03 6.66176e+04 -2.62275e+03 -4.95440e+05 2.59614e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.21941e+05 5.19149e+04 -3.70027e+05 -4.26341e+05 3.00052e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -6.53511e+02 1.16225e-06
- DD step 209999 vol min/aver 0.854 load imb.: force 3.5% pme mesh/force 1.618
- Step Time
- 210000 420.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.42143e+02 8.26495e+02 5.39051e+01 6.18132e+01 3.18381e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.11162e+03 6.47953e+04 -2.62275e+03 -4.94210e+05 2.62950e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22793e+05 5.19476e+04 -3.70846e+05 -4.26364e+05 3.00241e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.12907e+03 1.28335e-06
- DD step 219999 vol min/aver 0.862 load imb.: force 9.0% pme mesh/force 1.681
- Step Time
- 220000 440.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.68772e+02 8.49630e+02 2.47466e+01 3.67531e+01 2.85850e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.12368e+03 6.60565e+04 -2.62275e+03 -4.94902e+05 2.58430e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22294e+05 5.18227e+04 -3.70472e+05 -4.26340e+05 2.99519e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -7.92542e+02 1.32077e-06
- DD step 229999 vol min/aver 0.769 load imb.: force 7.0% pme mesh/force 1.668
- Step Time
- 230000 460.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.58857e+02 9.05539e+02 6.18351e+01 5.75491e+01 2.70445e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.09449e+03 6.58947e+04 -2.62275e+03 -4.95737e+05 2.56480e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23252e+05 5.23729e+04 -3.70879e+05 -4.26343e+05 3.02699e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -9.31776e+02 1.20983e-06
- DD step 239999 vol min/aver 0.876 load imb.: force 7.4% pme mesh/force 1.629
- Step Time
- 240000 480.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.40357e+02 8.12912e+02 5.26005e+01 2.00570e+01 2.70810e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.07081e+03 6.60540e+04 -2.62275e+03 -4.96245e+05 2.50194e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23844e+05 5.17616e+04 -3.72083e+05 -4.26334e+05 2.99165e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -9.79823e+02 1.21086e-06
- DD step 249999 vol min/aver 0.799 load imb.: force 5.4% pme mesh/force 1.411
- Step Time
- 250000 500.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.28704e+02 8.68927e+02 7.35099e+01 2.61438e+01 2.32411e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.05470e+03 6.62132e+04 -2.62275e+03 -4.96219e+05 2.57929e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23565e+05 5.15494e+04 -3.72016e+05 -4.26329e+05 2.97939e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -8.20525e+02 1.23531e-06
- DD step 259999 vol min/aver 0.827 load imb.: force 9.0% pme mesh/force 1.581
- Step Time
- 260000 520.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.62460e+02 8.09991e+02 5.21439e+01 3.83512e+01 2.62797e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.07602e+03 6.64889e+04 -2.62275e+03 -4.95934e+05 2.56524e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23001e+05 5.17591e+04 -3.71242e+05 -4.26326e+05 2.99151e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -8.20384e+02 1.11261e-06
- DD step 269999 vol min/aver 0.866 load imb.: force 5.8% pme mesh/force 1.550
- Step Time
- 270000 540.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.62757e+02 9.12090e+02 5.62107e+01 1.72326e+01 2.39519e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.02868e+03 6.59665e+04 -2.62275e+03 -4.95225e+05 2.49561e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22869e+05 5.23109e+04 -3.70558e+05 -4.26302e+05 3.02340e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -9.33155e+02 1.33632e-06
- DD step 279999 vol min/aver 0.800 load imb.: force 4.0% pme mesh/force 1.613
- Step Time
- 280000 560.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.48800e+02 8.27957e+02 4.81323e+01 7.98191e+00 2.35326e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.03502e+03 6.55403e+04 -2.62275e+03 -4.94719e+05 2.55864e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22839e+05 5.18468e+04 -3.70992e+05 -4.26308e+05 2.99658e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.05402e+03 1.49640e-06
- DD step 289999 vol min/aver 0.814 load imb.: force 5.6% pme mesh/force 1.655
- Step Time
- 290000 580.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.10537e+02 8.87622e+02 5.69040e+01 4.07754e+00 2.54655e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.10105e+03 6.57219e+04 -2.62275e+03 -4.94863e+05 2.47439e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22775e+05 5.21227e+04 -3.70652e+05 -4.26308e+05 3.01253e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.01462e+03 1.44348e-06
- DD step 299999 vol min/aver 0.849 load imb.: force 4.0% pme mesh/force 1.680
- Step Time
- 300000 600.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.35960e+02 8.49085e+02 4.95551e+01 2.86609e+01 2.44244e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.02728e+03 6.59180e+04 -2.62275e+03 -4.95682e+05 2.54417e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23408e+05 5.07241e+04 -3.72684e+05 -4.26296e+05 2.93170e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.01293e+03 1.45703e-06
- DD step 309999 vol min/aver 0.792 load imb.: force 7.7% pme mesh/force 1.654
- Step Time
- 310000 620.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.79550e+02 8.21869e+02 4.23894e+01 2.67873e+01 2.28741e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.03145e+03 6.57536e+04 -2.62275e+03 -4.94328e+05 2.47416e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22292e+05 5.22468e+04 -3.70046e+05 -4.26304e+05 3.01970e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -8.81644e+02 1.35911e-06
- DD step 319999 vol min/aver 0.819 load imb.: force 4.0% pme mesh/force 1.542
- Step Time
- 320000 640.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.34595e+02 9.04364e+02 7.52962e+01 3.77478e+01 2.91130e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.06777e+03 6.48789e+04 -2.62275e+03 -4.93625e+05 2.55573e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22202e+05 5.18243e+04 -3.70378e+05 -4.26285e+05 2.99528e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.12284e+03 1.24230e-06
- DD step 329999 vol min/aver 0.831 load imb.: force 4.7% pme mesh/force 1.741
- Step Time
- 330000 660.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.10282e+02 8.51836e+02 6.74899e+01 4.42646e+01 2.60894e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.08878e+03 6.60451e+04 -2.62275e+03 -4.94720e+05 2.55338e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22221e+05 5.20341e+04 -3.70187e+05 -4.26288e+05 3.00741e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -9.26365e+02 1.29566e-06
- DD step 339999 vol min/aver 0.804 load imb.: force 4.2% pme mesh/force 1.488
- Step Time
- 340000 680.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.28929e+02 8.35112e+02 4.32736e+01 3.29489e+01 2.40315e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 4.98391e+03 6.50579e+04 -2.62275e+03 -4.93592e+05 2.50750e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22285e+05 5.19001e+04 -3.70385e+05 -4.26290e+05 2.99966e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.13730e+03 1.27468e-06
- DD step 349999 vol min/aver 0.833 load imb.: force 4.6% pme mesh/force 1.737
- Step Time
- 350000 700.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.36201e+02 7.86544e+02 4.36519e+01 5.44619e+01 2.71932e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.06541e+03 6.53469e+04 -2.62275e+03 -4.93528e+05 2.55160e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.21794e+05 5.24764e+04 -3.69318e+05 -4.26294e+05 3.03297e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -8.61437e+02 1.24392e-06
- DD step 359999 vol min/aver 0.827 load imb.: force 6.6% pme mesh/force 1.453
- Step Time
- 360000 720.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 1.96544e+02 8.48812e+02 5.82798e+01 -4.97978e+00 2.73576e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.09435e+03 6.53636e+04 -2.62275e+03 -4.94258e+05 2.57112e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22479e+05 5.21529e+04 -3.70326e+05 -4.26295e+05 3.01428e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.03537e+03 1.32010e-06
- DD step 369999 vol min/aver 0.823 load imb.: force 16.8% pme mesh/force 1.925
- Step Time
- 370000 740.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.79447e+02 8.31308e+02 7.77932e+01 4.09314e+01 2.41514e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.09018e+03 6.55217e+04 -2.62275e+03 -4.94781e+05 2.53491e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22786e+05 5.22080e+04 -3.70578e+05 -4.26276e+05 3.01746e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -9.97834e+02 1.16491e-06
- DD step 379999 vol min/aver 0.835 load imb.: force 10.4% pme mesh/force 1.727
- Step Time
- 380000 760.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.71396e+02 8.64702e+02 4.17204e+01 -2.26017e+01 2.28892e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.10660e+03 6.64240e+04 -2.62275e+03 -4.95876e+05 2.46688e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23117e+05 5.19892e+04 -3.71128e+05 -4.26275e+05 3.00481e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -8.48042e+02 1.29718e-06
- DD step 389999 vol min/aver 0.886 load imb.: force 4.8% pme mesh/force 1.536
- Step Time
- 390000 780.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.31007e+02 9.24487e+02 1.00445e+02 2.66370e+01 2.63921e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.07572e+03 6.56874e+04 -2.62275e+03 -4.95669e+05 2.49512e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23487e+05 5.17500e+04 -3.71737e+05 -4.26281e+05 2.99099e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.01886e+03 1.16932e-06
- DD step 399999 vol min/aver 0.790 load imb.: force 2.9% pme mesh/force 1.623
- Step Time
- 400000 800.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.42584e+02 8.08286e+02 5.84265e+01 2.24787e+01 2.46780e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.01305e+03 6.50427e+04 -2.62275e+03 -4.94474e+05 2.50698e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23155e+05 5.17978e+04 -3.71357e+05 -4.26289e+05 2.99375e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.14416e+03 1.33881e-06
- DD step 409999 vol min/aver 0.820 load imb.: force 7.0% pme mesh/force 1.719
- Step Time
- 410000 820.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.55219e+02 8.90880e+02 9.27021e+01 4.06968e+01 2.63568e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.14654e+03 6.56352e+04 -2.62275e+03 -4.94481e+05 2.49502e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22284e+05 5.14659e+04 -3.70818e+05 -4.26272e+05 2.97457e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -8.52130e+02 1.29305e-06
- DD step 419999 vol min/aver 0.828 load imb.: force 5.8% pme mesh/force 1.780
- Step Time
- 420000 840.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.64515e+02 9.15444e+02 4.72084e+01 -2.48946e-02 2.80004e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.13217e+03 6.52254e+04 -2.62275e+03 -4.94716e+05 2.62324e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22850e+05 5.17900e+04 -3.71060e+05 -4.26270e+05 2.99330e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.10020e+03 1.42180e-06
- DD step 429999 vol min/aver 0.794 load imb.: force 6.2% pme mesh/force 1.515
- Step Time
- 430000 860.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.32342e+02 8.55095e+02 7.07176e+01 3.48133e+01 2.46329e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.06652e+03 6.64026e+04 -2.62275e+03 -4.95786e+05 2.55710e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22943e+05 5.19439e+04 -3.71000e+05 -4.26272e+05 3.00220e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -9.08260e+02 1.29182e-06
- DD step 439999 vol min/aver 0.816 load imb.: force 8.7% pme mesh/force 1.722
- Step Time
- 440000 880.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.91747e+02 8.51897e+02 5.81535e+01 1.40027e+01 2.35604e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.07194e+03 6.48898e+04 -2.62275e+03 -4.93306e+05 2.58562e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.21930e+05 5.12569e+04 -3.70673e+05 -4.26273e+05 2.96249e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.08407e+03 1.30449e-06
- DD step 449999 vol min/aver 0.766 load imb.: force 5.7% pme mesh/force 1.658
- Step Time
- 450000 900.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.99214e+02 8.32509e+02 6.68594e+01 -9.78734e+00 2.67082e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.07624e+03 6.57714e+04 -2.62275e+03 -4.95771e+05 2.50908e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23581e+05 5.21360e+04 -3.71445e+05 -4.26269e+05 3.01330e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.06368e+03 1.29658e-06
- DD load balancing is limited by minimum cell size in dimension Y
- DD step 459999 vol min/aver 0.832! load imb.: force 7.2% pme mesh/force 1.722
- Step Time
- 460000 920.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.60207e+02 8.95190e+02 4.40810e+01 1.58321e+01 2.50058e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.10301e+03 6.57602e+04 -2.62275e+03 -4.94722e+05 2.52403e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22492e+05 5.24061e+04 -3.70086e+05 -4.26266e+05 3.02890e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -9.84153e+02 1.17320e-06
- DD step 469999 vol min/aver 0.823 load imb.: force 8.3% pme mesh/force 1.677
- Step Time
- 470000 940.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.68064e+02 8.76732e+02 5.53627e+01 1.22674e+01 2.61426e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.13492e+03 6.64356e+04 -2.62275e+03 -4.95162e+05 2.53862e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22202e+05 5.15088e+04 -3.70694e+05 -4.26235e+05 2.97704e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -6.16632e+02 1.33242e-06
- DD step 479999 vol min/aver 0.806 load imb.: force 4.0% pme mesh/force 1.702
- Step Time
- 480000 960.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 3.25108e+02 8.28924e+02 4.24795e+01 6.00288e+01 2.46319e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.11839e+03 6.53210e+04 -2.62275e+03 -4.94022e+05 2.58092e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22122e+05 5.19144e+04 -3.70207e+05 -4.26241e+05 3.00049e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.05570e+03 1.30069e-06
- DD step 489999 vol min/aver 0.736 load imb.: force 5.2% pme mesh/force 1.704
- Step Time
- 490000 980.00000
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.87984e+02 8.30154e+02 7.83333e+01 3.83082e+01 2.30068e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.03306e+03 6.52440e+04 -2.62275e+03 -4.93817e+05 2.61520e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22083e+05 5.17565e+04 -3.70326e+05 -4.26230e+05 2.99136e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.02779e+03 1.31726e-06
- DD step 499999 vol min/aver 0.780 load imb.: force 4.4% pme mesh/force 1.597
- Step Time
- 500000 1000.00000
- Writing checkpoint, step 500000 at Sat Jun 5 19:35:36 2021
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.14297e+02 9.14571e+02 4.05245e+01 -6.60391e+00 2.46421e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.04188e+03 6.61173e+04 -2.62275e+03 -4.95430e+05 2.53993e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.22944e+05 5.20744e+04 -3.70870e+05 -4.26222e+05 3.00974e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -8.57011e+02 1.43072e-06
- Energy conservation over simulation part #1 of length 1000 ns, time 0 to 1000 ns
- Conserved energy drift: 2.97e-05 kJ/mol/ps per atom
- <====== ############### ==>
- <==== A V E R A G E S ====>
- <== ############### ======>
- Statistics over 500001 steps using 51 frames
- Energies (kJ/mol)
- Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
- 2.46717e+02 8.45758e+02 5.64148e+01 4.35527e+01 2.60359e+02
- Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
- 5.08330e+03 6.59721e+04 -2.62275e+03 -4.96247e+05 2.56202e+03
- Potential Kinetic En. Total Energy Conserved En. Temperature
- -4.23800e+05 5.18907e+04 -3.71909e+05 -4.26329e+05 2.99912e+02
- Pres. DC (bar) Pressure (bar) Constr. rmsd
- -2.01434e+02 -1.01623e+03 0.00000e+00
- Total Virial (kJ/mol)
- 2.38989e+04 1.58331e+02 -1.67534e+02
- 1.58287e+02 2.39290e+04 9.19167e+01
- -1.67521e+02 9.19728e+01 2.39353e+04
- Pressure (bar)
- -1.01184e+03 -2.51808e+01 2.20000e+01
- -2.51739e+01 -1.02016e+03 -1.17192e+01
- 2.19981e+01 -1.17278e+01 -1.01669e+03
- T-Protein T-non-Protein
- 2.98009e+02 2.99957e+02
- M E G A - F L O P S A C C O U N T I N G
- NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
- RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
- W3=SPC/TIP3p W4=TIP4p (single or pairs)
- V&F=Potential and force V=Potential only F=Force only
- Computing: M-Number M-Flops % Flops
- -----------------------------------------------------------------------------
- Pair Search distance check 170009.888240 1530088.994 0.2
- NxN Ewald Elec. + LJ [F] 5338683.455792 352353108.082 51.4
- NxN Ewald Elec. + LJ [V&F] 544.332368 58243.563 0.0
- NxN Ewald Elec. [F] 5128977.323760 312867616.749 45.6
- NxN Ewald Elec. [V&F] 522.698928 43906.710 0.0
- 1,4 nonbonded interactions 410.000820 36900.074 0.0
- Calc Weights 30871.561743 1111376.223 0.2
- Spread Q Bspline 658593.317184 1317186.634 0.2
- Gather F Bspline 658593.317184 3951559.903 0.6
- 3D-FFT 1395170.790336 11161366.323 1.6
- Solve PME 1936.003872 123904.248 0.0
- Reset In Box 257.283081 771.849 0.0
- CG-CoM 257.303662 771.911 0.0
- Bonds 90.000180 5310.011 0.0
- Angles 310.000620 52080.104 0.0
- Propers 20.000040 4580.009 0.0
- RB-Dihedrals 330.000660 81510.163 0.0
- Virial 1.104711 19.885 0.0
- Stop-CM 1.070212 10.702 0.0
- Calc-Ekin 2058.141162 55569.811 0.0
- Lincs 90.000540 5400.032 0.0
- Lincs-Mat 600.003600 2400.014 0.0
- Constraint-V 10150.540602 91354.865 0.0
- Constraint-Vir 1.026171 24.628 0.0
- Settle 3323.519941 1229702.378 0.2
- -----------------------------------------------------------------------------
- Total 686084763.868 100.0
- -----------------------------------------------------------------------------
- D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
- av. #atoms communicated per step for force: 2 x 85547.0
- Dynamic load balancing report:
- DLB was permanently on during the run per user request.
- Average load imbalance: 6.1%.
- The balanceable part of the MD step is 53%, load imbalance is computed from this.
- Part of the total run time spent waiting due to load imbalance: 3.3%.
- Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 %
- Average PME mesh/force load: 1.609
- Part of the total run time spent waiting due to PP/PME imbalance: 25.8 %
- NOTE: 25.8 % performance was lost because the PME ranks
- had more work to do than the PP ranks.
- You might want to increase the number of PME ranks
- or increase the cut-off and the grid spacing.
- 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
- On 24 MPI ranks doing PP, each using 4 OpenMP threads, and
- on 8 MPI ranks doing PME, each using 4 OpenMP threads
- Computing: Num Num Call Wall time Giga-Cycles
- Ranks Threads Count (s) total sum %
- -----------------------------------------------------------------------------
- Domain decomp. 24 4 12501 16.417 3301.993 1.9
- DD comm. load 24 4 12500 0.149 29.882 0.0
- DD comm. bounds 24 4 12501 1.373 276.193 0.2
- Send X to PME 24 4 500001 1.357 272.890 0.2
- Neighbor search 24 4 12501 19.693 3960.957 2.2
- Comm. coord. 24 4 487500 76.302 15346.816 8.7
- Force 24 4 500001 249.118 50105.781 28.3
- Wait + Comm. F 24 4 500001 71.082 14296.879 8.1
- PME mesh * 8 4 500001 596.020 39959.752 22.6
- PME wait for PP * 62.956 4220.853 2.4
- Wait + Recv. PME F 24 4 500001 191.683 38553.754 21.8
- NB X/F buffer ops. 24 4 1475001 15.307 3078.643 1.7
- Write traj. 24 4 51 0.107 21.422 0.0
- Update 24 4 500001 2.811 565.377 0.3
- Constraints 24 4 500003 4.654 936.007 0.5
- Comm. energies 24 4 50001 6.291 1265.414 0.7
- Rest 2.815 566.250 0.3
- -----------------------------------------------------------------------------
- Total 659.157 176771.013 100.0
- -----------------------------------------------------------------------------
- (*) Note that with separate PME ranks, the walltime column actually sums to
- twice the total reported, but the cycle count total and % are correct.
- -----------------------------------------------------------------------------
- Breakdown of PME mesh computation
- -----------------------------------------------------------------------------
- PME redist. X/F 8 4 1000002 182.735 12251.344 6.9
- PME spread 8 4 500001 103.814 6960.109 3.9
- PME gather 8 4 500001 68.290 4578.446 2.6
- PME 3D-FFT 8 4 1000002 49.863 3343.004 1.9
- PME 3D-FFT Comm. 8 4 2000004 184.824 12391.377 7.0
- PME solve Elec 8 4 500001 5.211 349.360 0.2
- -----------------------------------------------------------------------------
- Core t (s) Wall t (s) (%)
- Time: 84371.660 659.157 12799.9
- (ns/day) (hour/ns)
- Performance: 131.077 0.183
- Finished mdrun on rank 0 Sat Jun 5 19:35:36 2021
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