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embed_2018.log

log of the failed embedding simulation - Daniel Bauer, 12/22/2017 01:22 PM

 
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grompp
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Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
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NOTE 1 [file g_membed.mdp]:
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  The group cutoff scheme is deprecated since GROMACS 5.0 and will be
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  removed in a future release when all interaction forms are supported for
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  the verlet scheme. The verlet scheme already scales better, and it is
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  compatible with GPUs and other accelerators.
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NOTE 2 [file g_membed.mdp]:
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  With exact cut-offs, rlist should be larger than rcoulomb and rvdw, so
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  that there is a buffer region for particle motion between neighborsearch
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  steps
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NOTE 3 [file g_membed.mdp]:
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  For energy conservation with switch/shift potentials, rlist should be 0.1
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  to 0.3 nm larger than rvdw.
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Setting the LD random seed to -1633721488
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Generated 97877 of the 97903 non-bonded parameter combinations
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Generating 1-4 interactions: fudge = 1
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Generated 64492 of the 97903 1-4 parameter combinations
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Excluding 3 bonded neighbours molecule type 'kcsa'
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Excluding 3 bonded neighbours molecule type 'POPC'
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Excluding 3 bonded neighbours molecule type 'POPC'
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Excluding 2 bonded neighbours molecule type 'SOL'
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Excluding 1 bonded neighbours molecule type 'K'
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Excluding 1 bonded neighbours molecule type 'CL'
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NOTE 4 [file system.top, line 19]:
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  System has non-zero total charge: 4.000000
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  Total charge should normally be an integer. See
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  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
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  for discussion on how close it should be to an integer.
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WARNING 1 [file system.top, line 19]:
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  You are using Ewald electrostatics in a system with net charge. This can
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  lead to severe artifacts, such as ions moving into regions with low
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  dielectric, due to the uniform background charge. We suggest to
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  neutralize your system with counter ions, possibly in combination with a
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  physiological salt concentration.
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turning H bonds into constraints...
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turning H bonds into constraints...
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turning H bonds into constraints...
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turning H bonds into constraints...
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turning H bonds into constraints...
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
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Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net
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Charge
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J. Chem. Theory Comput. 10 (2014) pp. 381-393
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-------- -------- --- Thank You --- -------- --------
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Velocities were taken from a Maxwell distribution at 298 K
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Number of degrees of freedom in T-Coupling group Other is 63997.00
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Number of degrees of freedom in T-Coupling group Water_and_ions is 63045.00
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Number of degrees of freedom in T-Coupling group Protein is 0.00
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WARNING 2 [file g_membed.mdp]:
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  Can not exclude the lattice Coulomb energy between energy groups
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NOTE 5 [file g_membed.mdp]:
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  The sum of the two largest charge group radii (0.157881) is larger than
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  rlist (1.200000) - rvdw (1.200000).
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  With exact cut-offs, better performance can be obtained with
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  cutoff-scheme = Verlet, because it does not use charge groups at all.
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Estimate for the relative computational load of the PME mesh part: 0.07
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There were 5 notes
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There were 2 warnings
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Back Off! I just backed up g_membed.tpr to ./#g_membed.tpr.3#
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Analysing residue names:
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There are:   388    Protein residues
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There are:   200      Other residues
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There are: 10480      Water residues
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There are:    56        Ion residues
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Analysing Protein...
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Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
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Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
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Largest charge group radii for Van der Waals: 0.079, 0.079 nm
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Largest charge group radii for Coulomb:       0.079, 0.079 nm
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Calculating fourier grid dimensions for X Y Z
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Using a fourier grid of 72x72x80, spacing 0.108 0.108 0.120
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This run will generate roughly 6 Mb of data
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Copy input topology to output topology
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Run embedding simulation
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Compiled SIMD: AVX_256, but for this host/run AVX2_128 might be better (see
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log).
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Reading file g_membed.tpr, VERSION 2018-beta1 (single precision)
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NOTE: GPU(s) found, but the current simulation can not use GPUs
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      To use a GPU, set the mdp option: cutoff-scheme = Verlet
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Membrane embedding only supports a single rank. Choosing to use only a single thread-MPI rank.
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Using 1 MPI thread
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Initializing membed
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Setting -cpt to -1, because embedding cannot be restarted from cpt-files.
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Select a group to embed in the membrane:
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Group     0 (         System) has 64175 elements
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Group     1 (        Protein) has  5879 elements
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Group     2 (      Protein-H) has  2901 elements
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Group     3 (        C-alpha) has   388 elements
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Group     4 (       Backbone) has  1164 elements
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Group     5 (      MainChain) has  1551 elements
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Group     6 (   MainChain+Cb) has  1899 elements
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Group     7 (    MainChain+H) has  1929 elements
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Group     8 (      SideChain) has  3950 elements
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Group     9 (    SideChain-H) has  1350 elements
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Group    10 (    Prot-Masses) has  5879 elements
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Group    11 (    non-Protein) has 58296 elements
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Group    12 (          Other) has 26800 elements
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Group    13 (           POPC) has 26800 elements
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Group    14 (              K) has    28 elements
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Group    15 (             CL) has    28 elements
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Group    16 (          Water) has 31440 elements
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Group    17 (            SOL) has 31440 elements
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Group    18 (      non-Water) has 32735 elements
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Group    19 (            Ion) has    56 elements
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Group    20 (           POPC) has 26800 elements
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Group    21 (              K) has    28 elements
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Group    22 (             CL) has    28 elements
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Group    23 ( Water_and_ions) has 31496 elements
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Select a group: 
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Select a group to embed Protein into (e.g. the membrane):
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Group     0 (         System) has 64175 elements
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Group     1 (        Protein) has  5879 elements
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Group     2 (      Protein-H) has  2901 elements
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Group     3 (        C-alpha) has   388 elements
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Group     4 (       Backbone) has  1164 elements
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Group     5 (      MainChain) has  1551 elements
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Group     6 (   MainChain+Cb) has  1899 elements
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Group     7 (    MainChain+H) has  1929 elements
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Group     8 (      SideChain) has  3950 elements
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Group     9 (    SideChain-H) has  1350 elements
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Group    10 (    Prot-Masses) has  5879 elements
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Group    11 (    non-Protein) has 58296 elements
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Group    12 (          Other) has 26800 elements
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Group    13 (           POPC) has 26800 elements
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Group    14 (              K) has    28 elements
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Group    15 (             CL) has    28 elements
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Group    16 (          Water) has 31440 elements
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Group    17 (            SOL) has 31440 elements
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Group    18 (      non-Water) has 32735 elements
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Group    19 (            Ion) has    56 elements
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Group    20 (           POPC) has 26800 elements
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Group    21 (              K) has    28 elements
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Group    22 (             CL) has    28 elements
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Group    23 ( Water_and_ions) has 31496 elements
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Select a group: Embedding piece 0 with center of geometry: 3.892237 3.892237 4.296000
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Back Off! I just backed up temp.topwzNoUM to ./#temp.topwzNoUM.1#
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Back Off! I just backed up embedded.top to ./#embedded.top.1#
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NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
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removed in a future release when 'verlet' supports all interaction forms.
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Back Off! I just backed up g_membed.xtc to ./#g_membed.xtc.1#
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Back Off! I just backed up g_membed.edr to ./#g_membed.edr.1#
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starting mdrun 'KcsA in POPC'
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1000 steps,      2.0 ps.
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step 0: One or more water molecules can not be settled.
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Check for bad contacts and/or reduce the timestep if appropriate.
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Wrote pdb files with previous and current coordinates
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Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
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         Box (3x3):
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            Box[    0]={        -nan,         -nan,         -nan}
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            Box[    1]={        -nan,         -nan,         -nan}
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            Box[    2]={        -nan,         -nan,         -nan}
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         Can not fix pbc.
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