[gmx-users] genion writes a log file?

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 18 21:38:17 CET 2010


Hi,

When using versions 4.5.2 and 4.5.3, I have noticed that genion now outputs a 
file called "genion.log" (or "genion_node0.log" with 4.5.2) that appears to 
contain the header information normally found in an md.log file produced by 
mdrun (see below).  Is this normal?  There really isn't any use to this file, 
from what I can tell, so I suspect it shouldn't be written, but I can't find the 
relevant code change that would have caused it.

-Justin

genion.log:
===========
Log file opened on Thu Nov 18 15:12:15 2010
Host: justin-lemkuls-macbook.local  pid: 19469  nodeid: 0  nnodes:  1
The Gromacs distribution was built Thu Nov 18 15:00:26 EST 2010 by
justin at justin-lemkuls-macbook.local (Darwin 9.8.0 i386)


Input Parameters:
    integrator           = steep
    nsteps               = 50000
    init_step            = 0
    ns_type              = Grid
    nstlist              = 1
    ndelta               = 2
    nstcomm              = 10
    comm_mode            = Linear
    nstlog               = 100
    nstxout              = 100
    nstvout              = 100
    nstfout              = 0
    nstcalcenergy        = -1
    nstenergy            = 100
    nstxtcout            = 0
    init_t               = 0
    delta_t              = 0.001
    xtcprec              = 1000
    nkx                  = 50
    nky                  = 54
    nkz                  = 48
    pme_order            = 4
    ewald_rtol           = 1e-05
    ewald_geometry       = 0
    epsilon_surface      = 0
    optimize_fft         = FALSE
    ePBC                 = xyz
    bPeriodicMols        = FALSE
    bContinuation        = FALSE
    bShakeSOR            = FALSE
    etc                  = No
    nsttcouple           = -1
    epc                  = No
    epctype              = Isotropic
    nstpcouple           = -1
    tau_p                = 1
    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}
    compress (3x3):
       compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
       compress[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
       compress[    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
    andersen_seed        = 815131
    rlist                = 1
    rlistlong            = 1
    rtpi                 = 0.05
    coulombtype          = PME
    rcoulomb_switch      = 0
    rcoulomb             = 1
    vdwtype              = Cut-off
    rvdw_switch          = 0
    rvdw                 = 1
    epsilon_r            = 1
    epsilon_rf           = 1
    tabext               = 1
    implicit_solvent     = No
    gb_algorithm         = Still
    gb_epsilon_solvent   = 80
    nstgbradii           = 1
    rgbradii             = 1
    gb_saltconc          = 0
    gb_obc_alpha         = 1
    gb_obc_beta          = 0.8
    gb_obc_gamma         = 4.85
    gb_dielectric_offset = 0.009
    sa_algorithm         = Ace-approximation
    sa_surface_tension   = 2.05016
    DispCorr             = No
    free_energy          = no
    init_lambda          = 0
    delta_lambda         = 0
    n_foreign_lambda     = 0
    sc_alpha             = 0
    sc_power             = 0
    sc_sigma             = 0.3
    sc_sigma_min         = 0.3
    nstdhdl              = 10
    separate_dhdl_file   = yes
    dhdl_derivatives     = yes
    dh_hist_size         = 0
    dh_hist_spacing      = 0.1
    nwall                = 0
    wall_type            = 9-3
    wall_atomtype[0]     = -1
    wall_atomtype[1]     = -1
    wall_density[0]      = 0
    wall_density[1]      = 0
    wall_ewald_zfac      = 3
    pull                 = no
    disre                = No
    disre_weighting      = Conservative
    disre_mixed          = FALSE
    dr_fc                = 1000
    dr_tau               = 0
    nstdisreout          = 100
    orires_fc            = 0
    orires_tau           = 0
    nstorireout          = 100
    dihre-fc             = 1000
    em_stepsize          = 0.01
    em_tol               = 1000
    niter                = 20
    fc_stepsize          = 0
    nstcgsteep           = 1000
    nbfgscorr            = 10
    ConstAlg             = Lincs
    shake_tol            = 0.0001
    lincs_order          = 4
    lincs_warnangle      = 30
    lincs_iter           = 1
    bd_fric              = 0
    ld_seed              = 1993
    cos_accel            = 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}
    userint1             = 0
    userint2             = 0
    userint3             = 0
    userint4             = 0
    userreal1            = 0
    userreal2            = 0
    userreal3            = 0
    userreal4            = 0
grpopts:
    nrdf:       41373
    ref_t:           0
    tau_t:           0
anneal:          No
ann_npoints:           0
    acc:	           0           0           0
    nfreeze:           N           N           N
    energygrp_flags[  0]: 0
    efield-x:
       n = 0
    efield-xt:
       n = 0
    efield-y:
       n = 0
    efield-yt:
       n = 0
    efield-z:
       n = 0
    efield-zt:
       n = 0
    bQMMM                = FALSE
    QMconstraints        = 0
    QMMMscheme           = 0
    scalefactor          = 1
qm_opts:
    ngQM                 = 0
Max number of connections per atom is 102
Total number of connections is 87500
Max number of graph edges per atom is 4
Total number of graph edges is 27632
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     TRUE
Will do PME sum in reciprocal space.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, 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 --- -------- --------

Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Using shifted Lennard-Jones, switch between 0 and 1 nm
Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
System total charge: 8.000
Generated table with 1000 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ12Shift.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 LJ12.
Tabscale = 500 points/nm

Enabling SPC-like water optimization for 5916 molecules.

Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing ia32 SSE2 support... present.


Removing pbc first time
Done rmpbc


-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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