Commit 0f45cd61 authored by sjplimp's avatar sjplimp Committed by GitHub
Browse files

Merge pull request #196 from akohlmey/charmm-cmap-updates

Some more cmap-related updates for ch2lmp
parents 493873fb d7d321a5
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+34 −27
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@@ -8,7 +8,7 @@ lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.
In this directory, you should find:
1) A perl script called "charmm2lammps.pl"
2) A perl script called "lammps2pdb.pl"
3) An "example" folder containing an example of how to use these tools.
3) Two folders containing examples of how to use these tools.
4) An "other" folder containing other potentially useful tools.

In addition, you will need to provide the following input for
@@ -24,11 +24,11 @@ To use the charmm2lammps.pl script, type: "perl charmm2lammps.pl
<forcefield> <project> [-option=value ...]" where <forcefield> is the
name of the CHARMM FF you are using, (i.e. all22_prot), and <project>
is the common name of your *.crd and *.psf files.  Possible options
are listed next.  If the option requires a parameter, the syntax
should be -option=value (e.g. -border=5).
are listed below.  If the option requires a parameter, the syntax
must be like this: -option=value (e.g. -border=5).

-help        display available options
-charmm      add charmm types to LAMMPS data file
-nohints     do not add charmm types and style hints to LAMMPS data file
-water       add TIP3P water [default: 1 g/cc]
-ions        add (counter)ions using Na+ and Cl- [default: 0 mol/l]
-center      recenter atoms
@@ -42,7 +42,6 @@ should be -option=value (e.g. -border=5).
-ax          rotation around x-axis
-ay          rotation around y-axis
-az          rotation around z-axis
-cd          correction for dihedral for carbohydrate systems
-cmap        add CMAP section to data file and fix cmap command lines in
             input script" (NOTE: requires use of *.pdb file)

@@ -52,15 +51,16 @@ biomolecule and convert it into LAMMPS input, and then create a *.pdb
trajectory from the LAMMPS output.

1) Get the pdb file you want to model. http://www.rcsb.org/pdb/ For
this example, we will use 1ac7.pdb
this examples, we will use either 1ac7.pdb or 1gb1.pdb

2) If there are multiple models in the pdb file, choose the one you
want and delete the others. Save the pared-down file as 1ac7_pared.pdb

3) Download the charmm FF files and choose the one you want from the
tarball.  We will use all27_na for this example.
http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm
toppar_c31b1.tar.gz
tarball.  We will use all27_na for 1AC7 and all36_prot for 1GB1. The
required files for the example are included in their folders. You can
download complete CHARMM force field packages from:
http://mackerell.umaryland.edu/charmm_ff.shtml

4) Create a *.pgn file for use with psfgen (you will need to have VMD
installed, http://www.ks.uiuc.edu/Research/vmd/ ). This is the hardest
@@ -85,44 +85,50 @@ writepdb 1ac7.pdb
writepsf charmm 1ac7.psf
exit

5) Type "vmd -e 1ac7.pgn" to build the 1ac7.psf file, and the new
For 1GB1 the corresponding 1gb1.psf file has been created with CHARMM-GUI,
http://www.charmm-gui.org

5) Type "vmd -dispdev none -e 1ac7.pgn" to build the 1ac7.psf file, and the new
   1ac7.pdb file.

6) Run charmm2lammps.pl by typing:
"perl charmm2lammps.pl all27_na 1ac7 -charmm -border=1 -pdb_ctrl -water -ions"
"perl charmm2lammps.pl all27_na 1ac7 -border=2.0 -pdb_ctrl -water -ions"
or
"perl charmm2lammps.pl all36_prot 1gb1 -border=2.0 -cmap=36 -water -ions"

7) Run lammps by typing: "lmp < 1ac7.in"
7) Run lammps by typing: "lmp_mpi -in 1ac7.in" or "lmp_mpi -in 1gb1.in"

8) Run lammps2pdb.pl by typing: "perl lammps2pdb.pl 1ac7"

** Additional notes:

The charmm2lammps.pl script takes the pdb and psf files for the 1ac7
molecule and converts them into LAMMPS format. The -water option
or 1gb1 molecules and converts them into LAMMPS format. The -water option
embeds the molecule in water on a crystal lattice. The -border option
includes a layer of water surrounding the minimum dimensions of the
molecule. The -pdb_ctrl option produces the 1ac7_ctrl.pdb file that
can be visualized in a standard visualization package such as VMD. The
-charmm option put comments into the LAMMPS data file (everything
can be visualized in a standard visualization package such as VMD. By
default, comments are added into the LAMMPS data file (everything
after the # sign is a comment) for user convenience in tracking atom
types etc. according to CHARMM nomenclature.
types etc. according to CHARMM nomenclature. If this is not desired,
the -nohints option can be used to turn off this function.

The example molecule provided above (i.e., 1ac7) is a DNA fragment.
If instead, a peptide longer than 2 amino acid residues or a protein
is to be modeled, the '-cmap' option should be used. This will add a
section at the end of the data file with the heading of 'CMAP' that
The provided 1ac7 example molecule is a DNA fragment. For peptides
longer than 2 amino acid residues or a protein is to be modeled,
e.g. the 1gb1 binding domain of a protein, the '-cmap' option should
be used. This will add CMAP section at the end of the data file that
will contain cmap crossterm corrections for the phi-psi dihedrals for
the amino acid residues. You will then need to also copy the
appropriate file for the cmap crossterms into your directory and be
sure that you are using the appropriate cmap crossterms that go with
the respective version of the charmm force field that is being used
(e.g, cmap22.data or cmap36.data). This is necessary to account for
the fact that the CHARMM group has provided updated cmap correction
(e.g, charmm22.cmap or charmm36.cmap). This is necessary to account
for the fact that the CHARMM group has provided updated cmap correction
terms for use with the c36 and more recent version of the charmm
protein force field.  Copies of cmap22.data and cmap36.data are
provided in the tools/ch2lmp directory.
protein force field.  Copies of charmm22.cmap and charmm36.cmap are
provided in the potentials directory.

The default timestep in the LAMMPS *.in file is set to 0.5 fs, which
The default timestep in the LAMMPS *.in file is set to 1.0 fs, which
can typically be increased to 2 fs after equilibration if the bonds
involving H are constrained via shake. Also, after equilibration, the
delay on neigh_modify can probably increased to 5 or so to improve
@@ -131,7 +137,7 @@ speed.
The -ions option allows the user to neutralize the simulation cell
with Na+ or Cl- counterions if the molecule has a net charge
Additional salt can be added by increasing the default concentration
(e.g. -ions=0.5).
(i.e., -ions=0.5).

** In the "other" file folder, you will find:

@@ -146,3 +152,4 @@ Additional salt can be added by increasing the default concentration
3) A 3rd party perl script called "crd2pdb.pl"

4) A 3rd party fortran code called "pdb_to_crd.f"
+657 −650
Original line number Diff line number Diff line
@@ -38,6 +38,7 @@
#    20161001   Added 'CMAP crossterms' section at the end of the data file
#    20161001   Added instructions in CMAP section to fix problem if 'ter'
#                 is not designated in the .pdb file to identify last amino acid
#    20161005   Added tweak to embed command line in generated LAMMPS input
#
#    General    Many thanks to Paul S. Crozier for checking script validity
#               against his projects.
@@ -85,7 +86,7 @@
    my $notes;

    $program            = "charmm2lammps";
    $version		= "1.9.0";
    $version            = "1.9.1";
    $year               = "2016";
    $add                = 1;
    $water_dens         = 0;
@@ -120,6 +121,9 @@
    $notes .= "      - project.in            suggested LAMMPS input script\n";
    $notes .= "      - project_ctrl.pdb      control file when requested\n";

    # record full command line for later use
    $cmdline = "$program.pl " . join(" ",@ARGV);

    foreach (@ARGV)
    {
      if (substr($_, 0, 1) eq "-")
@@ -1437,7 +1441,8 @@
  sub WriteLAMMPSInput
  {
    open(LAMMPS, ">$project.in");                       # input file
    printf(LAMMPS "# Created by $program v$version on %s\n", `date`);
    printf(LAMMPS "# Created by $program v$version on %s", `date`);
    printf(LAMMPS "# Command: %s\n\n", $cmdline);
    printf(LAMMPS "units           real\n");            # general
    printf(LAMMPS "neigh_modify    delay 2 every 1\n\n");
    printf(LAMMPS "atom_style      full\n");            # styles
@@ -1467,20 +1472,22 @@
      printf(LAMMPS "\n");
    }
    printf(LAMMPS "special_bonds   charmm\n");          # invoke charmm
    printf(LAMMPS "thermo          1\n");		# set thermo style
    printf(LAMMPS "thermo          10\n");              # set thermo style
    printf(LAMMPS "thermo_style    multi\n");
    printf(LAMMPS "timestep        0.5\n\n");		# 0.5 ps time step
    printf(LAMMPS "minimize 0.0 0.0 1000 10000\n\n");   # take off the edge
    printf(LAMMPS "timestep        1.0\n\n");           # 1.0 ps time step
    printf(LAMMPS "minimize 0.0 0.0 50 200\n\n");       # take of the edge
    printf(LAMMPS "reset_timestep  0\n");
    printf(LAMMPS "fix             1 all nve\n");
    printf(LAMMPS "fix             2 all shake 1e-6 500 0 m 1.0\n")
      if ($shake eq "");                                # shake all H-bonds
    printf(LAMMPS "fix             2 all shake 1e-6 500 0 m 1.0 a %s\n",$shake)
      if ($shake ne "");                                # add water if present
    printf(LAMMPS "velocity        all create 0.0 12345678 dist uniform\n\n");
    printf(LAMMPS "restart         10 $project.restart1 $project.restart2\n");
    printf(LAMMPS "dump            1 all atom 10 $project.dump\n");
    printf(LAMMPS "restart         500 $project.restart1 $project.restart2\n");
    printf(LAMMPS "dump            1 all atom 100 $project.dump\n");
    printf(LAMMPS "dump_modify     1 image yes scale yes\n\n");
    printf(LAMMPS "run             20\n");		# run for 20 time steps
    printf(LAMMPS "thermo          100\n");		# set thermo style
    printf(LAMMPS "run             1000\n");		# run for 1000 time steps
    close(LAMMPS);
  }

+10614 −0

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+36 −0
Original line number Diff line number Diff line
# Created by charmm2lammps v1.9.1 on Wed Oct  5 18:08:55 EDT 2016
# Command: charmm2lammps.pl -water -ions -border=2.0 all36_prot 1gb1

units           real
neigh_modify    delay 2 every 1

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic

pair_style      lj/charmm/coul/long 8 12
pair_modify     mix arithmetic
kspace_style    pppm 1e-6

read_data       1gb1.data

special_bonds   charmm
thermo          10
thermo_style    multi
timestep        1.0

minimize 0.0 0.0 50 200

reset_timestep  0
fix             1 all nve
fix             2 all shake 1e-6 500 0 m 1.0 a 112
velocity        all create 0.0 12345678 dist uniform

restart         500 1gb1.restart1 1gb1.restart2
dump            1 all atom 100 1gb1.dump
dump_modify     1 image yes scale yes

thermo          100
run             1000
+256 −0
Original line number Diff line number Diff line
LAMMPS (5 Oct 2016)
package omp 0
WARNING: OpenMP support not enabled during compilation; using 1 thread only. (../fix_omp.cpp:123)
# Created by charmm2lammps v1.9.1 on Wed Oct  5 18:08:55 EDT 2016
# Command: charmm2lammps.pl -water -ions -border=2.0 all36_prot 1gb1

units           real
neigh_modify    delay 2 every 1

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic

pair_style      lj/charmm/coul/long 8 12
pair_modify     mix arithmetic
kspace_style    pppm 1e-6

read_data       1gb1.data
  orthogonal box = (-20.8413 -14.5892 -13.805) to (23.4963 14.9692 10.827)
  2 by 2 by 2 MPI processor grid
  reading atoms ...
  2833 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  24 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  reading bonds ...
  2177 bonds
  reading angles ...
  2209 angles
  reading dihedrals ...
  2707 dihedrals
  reading impropers ...
  137 impropers
  4 = max # of 1-2 neighbors
  9 = max # of 1-3 neighbors
  17 = max # of 1-4 neighbors
  21 = max # of special neighbors

special_bonds   charmm
thermo          10
thermo_style    multi
timestep        1.0

minimize 0.0 0.0 50 200
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
  G vector (1/distance) = 0.278254
  grid = 45 32 30
  stencil order = 5
  estimated absolute RMS force accuracy = 0.000317429
  estimated relative force accuracy = 9.55928e-07
  using double precision FFTs
  3d grid and FFT values/proc = 15180 5760
Last active /omp style is kspace_style pppm/omp
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7 -> bins = 7 5 4
Memory usage per processor = 19.7492 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =     -3599.1065 KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =     -3599.1065 E_bond   =       169.6834 E_angle  =       103.6483 
E_dihed  =       583.9669 E_impro  =         0.0335 E_vdwl   =      -776.0899 
E_coul   =     35419.6941 E_long   =    -39100.0428 Press    =      3623.5803 
---------------- Step       10 ----- CPU =      0.2563 (sec) ----------------
TotEng   =     -5168.1778 KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =     -5168.1778 E_bond   =       120.7538 E_angle  =       171.5023 
E_dihed  =       583.0143 E_impro  =         6.5958 E_vdwl   =     -1034.8022 
E_coul   =     34737.4006 E_long   =    -39752.6424 Press    =    -10232.1944 
---------------- Step       20 ----- CPU =      0.4597 (sec) ----------------
TotEng   =     -5784.4945 KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =     -5784.4945 E_bond   =       110.1359 E_angle  =       262.6659 
E_dihed  =       573.8164 E_impro  =         8.5071 E_vdwl   =     -1050.9646 
E_coul   =     34464.2659 E_long   =    -40152.9212 Press    =    -10843.0328 
---------------- Step       30 ----- CPU =      0.6813 (sec) ----------------
TotEng   =     -6342.0862 KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =     -6342.0862 E_bond   =       146.0247 E_angle  =       272.7224 
E_dihed  =       557.6616 E_impro  =         7.1074 E_vdwl   =      -984.4028 
E_coul   =     34031.1722 E_long   =    -40372.3718 Press    =    -13674.9873 
---------------- Step       40 ----- CPU =      0.8599 (sec) ----------------
TotEng   =     -6821.3956 KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =     -6821.3956 E_bond   =       147.4491 E_angle  =       271.5247 
E_dihed  =       548.2429 E_impro  =         7.1832 E_vdwl   =      -873.4714 
E_coul   =     33514.8072 E_long   =    -40437.1312 Press    =    -12024.8390 
---------------- Step       50 ----- CPU =      1.0662 (sec) ----------------
TotEng   =     -7278.3435 KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =     -7278.3435 E_bond   =       181.9934 E_angle  =       288.9107 
E_dihed  =       541.0050 E_impro  =         7.1673 E_vdwl   =      -501.3825 
E_coul   =     32665.6923 E_long   =    -40461.7297 Press    =    -10391.9829 
Loop time of 1.06631 on 8 procs for 50 steps with 2833 atoms

99.3% CPU use with 8 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = max iterations
  Energy initial, next-to-last, final = 
        -3599.10649881     -7238.80368107     -7278.34352699
  Force two-norm initial, final = 1109.81 247.325
  Force max component initial, final = 107.492 37.5055
  Final line search alpha, max atom move = 0.00133024 0.0498915
  Iterations, force evaluations = 50 87

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.46313    | 0.53526    | 0.61611    |   6.9 | 50.20
Bond    | 0.0070326  | 0.01008    | 0.013407   |   1.8 |  0.95
Kspace  | 0.3364     | 0.41785    | 0.49165    |   8.0 | 39.19
Neigh   | 0.035014   | 0.035175   | 0.035337   |   0.1 |  3.30
Comm    | 0.058533   | 0.05973    | 0.060792   |   0.3 |  5.60
Output  | 0.00039005 | 0.00040504 | 0.00049496 |   0.2 |  0.04
Modify  | 0.0015707  | 0.0022006  | 0.0025775  |   0.6 |  0.21
Other   |            | 0.005615   |            |       |  0.53

Nlocal:    354.125 ave 376 max 344 min
Histogram: 3 1 0 1 2 0 0 0 0 1
Nghost:    7405 ave 7531 max 7307 min
Histogram: 1 2 1 0 0 1 1 1 0 1
Neighs:    178281 ave 194848 max 158123 min
Histogram: 2 0 1 0 0 1 0 1 2 1

Total # of neighbors = 1426250
Ave neighs/atom = 503.442
Ave special neighs/atom = 4.67702
Neighbor list builds = 4
Dangerous builds = 0

reset_timestep  0
fix             1 all nve
fix             2 all shake 1e-6 500 0 m 1.0 a 112
  168 = # of size 2 clusters
  64 = # of size 3 clusters
  41 = # of size 4 clusters
  658 = # of frozen angles
velocity        all create 0.0 12345678 dist uniform

restart         500 1gb1.restart1 1gb1.restart2
dump            1 all atom 100 1gb1.dump
dump_modify     1 image yes scale yes

thermo          100
run             1000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
  G vector (1/distance) = 0.278254
  grid = 45 32 30
  stencil order = 5
  estimated absolute RMS force accuracy = 0.000317429
  estimated relative force accuracy = 9.55928e-07
  using double precision FFTs
  3d grid and FFT values/proc = 15180 5760
Last active /omp style is kspace_style pppm/omp
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 2 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7 -> bins = 7 5 4
Memory usage per processor = 20.5221 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =     -7547.0017 KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =     -7547.0017 E_bond   =        52.4535 E_angle  =       149.7924 
E_dihed  =       541.0050 E_impro  =         7.1673 E_vdwl   =      -501.3825 
E_coul   =     32665.6923 E_long   =    -40461.7297 Press    =     -9600.9476 
---------------- Step      100 ----- CPU =      0.8242 (sec) ----------------
TotEng   =     -7049.9503 KinEng   =       688.1123 Temp     =       113.4757 
PotEng   =     -7738.0625 E_bond   =        53.8035 E_angle  =       139.7846 
E_dihed  =       529.5460 E_impro  =         6.1806 E_vdwl   =        52.8666 
E_coul   =     31951.7370 E_long   =    -40471.9810 Press    =     -5991.4443 
---------------- Step      200 ----- CPU =      1.6765 (sec) ----------------
TotEng   =     -7050.0350 KinEng   =       956.0848 Temp     =       157.6667 
PotEng   =     -8006.1198 E_bond   =        47.1331 E_angle  =       140.9769 
E_dihed  =       517.5474 E_impro  =         5.7244 E_vdwl   =       635.2166 
E_coul   =     31127.8100 E_long   =    -40480.5282 Press    =      -920.9624 
---------------- Step      300 ----- CPU =      2.5246 (sec) ----------------
TotEng   =     -7050.0984 KinEng   =      1049.7346 Temp     =       173.1104 
PotEng   =     -8099.8330 E_bond   =        47.4551 E_angle  =       156.5090 
E_dihed  =       520.6006 E_impro  =         9.4008 E_vdwl   =       451.0904 
E_coul   =     31202.3817 E_long   =    -40487.2707 Press    =     -2352.9550 
---------------- Step      400 ----- CPU =      3.3982 (sec) ----------------
TotEng   =     -7050.1671 KinEng   =      1099.2465 Temp     =       181.2753 
PotEng   =     -8149.4136 E_bond   =        56.6375 E_angle  =       164.5897 
E_dihed  =       528.8356 E_impro  =         8.8390 E_vdwl   =       525.0114 
E_coul   =     31060.0380 E_long   =    -40493.3650 Press    =     -2146.9087 
---------------- Step      500 ----- CPU =      4.2800 (sec) ----------------
TotEng   =     -7050.2027 KinEng   =      1134.4924 Temp     =       187.0877 
PotEng   =     -8184.6951 E_bond   =        53.5903 E_angle  =       169.1090 
E_dihed  =       522.9488 E_impro  =         7.9830 E_vdwl   =       496.8404 
E_coul   =     31058.9967 E_long   =    -40494.1633 Press    =     -2537.1829 
---------------- Step      600 ----- CPU =      5.1548 (sec) ----------------
TotEng   =     -7050.1894 KinEng   =      1122.6756 Temp     =       185.1390 
PotEng   =     -8172.8649 E_bond   =        47.9283 E_angle  =       168.7967 
E_dihed  =       518.7200 E_impro  =         9.2011 E_vdwl   =       499.6778 
E_coul   =     31076.1916 E_long   =    -40493.3805 Press    =     -1939.2216 
---------------- Step      700 ----- CPU =      6.0377 (sec) ----------------
TotEng   =     -7050.2850 KinEng   =      1154.4452 Temp     =       190.3781 
PotEng   =     -8204.7301 E_bond   =        54.3594 E_angle  =       183.8772 
E_dihed  =       513.0797 E_impro  =         9.6842 E_vdwl   =       522.0052 
E_coul   =     31008.3632 E_long   =    -40496.0990 Press    =     -2059.4885 
---------------- Step      800 ----- CPU =      6.9161 (sec) ----------------
TotEng   =     -7050.2852 KinEng   =      1146.2741 Temp     =       189.0306 
PotEng   =     -8196.5593 E_bond   =        48.8126 E_angle  =       171.3411 
E_dihed  =       525.8682 E_impro  =        10.5588 E_vdwl   =       538.6905 
E_coul   =     31003.8447 E_long   =    -40495.6752 Press    =     -1458.5181 
---------------- Step      900 ----- CPU =      7.8101 (sec) ----------------
TotEng   =     -7050.3025 KinEng   =      1154.2134 Temp     =       190.3398 
PotEng   =     -8204.5159 E_bond   =        51.1010 E_angle  =       177.9642 
E_dihed  =       520.6908 E_impro  =         8.9539 E_vdwl   =       521.5994 
E_coul   =     31012.6307 E_long   =    -40497.4560 Press    =     -1683.9131 
---------------- Step     1000 ----- CPU =      8.7313 (sec) ----------------
TotEng   =     -7050.3166 KinEng   =      1179.9351 Temp     =       194.5816 
PotEng   =     -8230.2517 E_bond   =        57.8905 E_angle  =       190.1556 
E_dihed  =       518.1288 E_impro  =        10.0403 E_vdwl   =       557.6413 
E_coul   =     30933.6472 E_long   =    -40497.7554 Press    =     -1643.1247 
Loop time of 8.73139 on 8 procs for 1000 steps with 2833 atoms

Performance: 9.895 ns/day, 2.425 hours/ns, 114.529 timesteps/s
99.6% CPU use with 8 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.2841     | 3.856      | 4.393      |  17.3 | 44.16
Bond    | 0.041216   | 0.074389   | 0.11041    |   7.2 |  0.85
Kspace  | 2.8668     | 3.4354     | 4.0036     |  18.9 | 39.35
Neigh   | 0.3024     | 0.30315    | 0.30402    |   0.1 |  3.47
Comm    | 0.58794    | 0.60511    | 0.61362    |   1.0 |  6.93
Output  | 0.010607   | 0.010696   | 0.010783   |   0.0 |  0.12
Modify  | 0.40802    | 0.41482    | 0.42598    |   0.8 |  4.75
Other   |            | 0.03184    |            |       |  0.36

Nlocal:    354.125 ave 390 max 323 min
Histogram: 2 0 2 0 1 0 0 0 1 2
Nghost:    7219.12 ave 7453 max 6941 min
Histogram: 1 1 1 1 0 0 0 0 2 2
Neighs:    179095 ave 217661 max 144647 min
Histogram: 1 0 1 1 1 2 1 0 0 1

Total # of neighbors = 1432758
Ave neighs/atom = 505.739
Ave special neighs/atom = 4.67702
Neighbor list builds = 39
Dangerous builds = 0
Total wall time: 0:00:09
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