the log file just lists all the parameters of the simulation, following is a
part of it
parameters of the run:
integrator = md
nsteps = 4000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 0
comm_mode = Linear
nstlog = 1000
nstxout = 1000
nstvout = 0
nstfout = 500
nstenergy = 10
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xy
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = No
epc = No
epctype = Isotropic
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 = 1.3
rtpi = 0.05
coulombtype = Reaction-Field-zero
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Shift
rvdw_switch = 0.9
rvdw = 1
epsilon_r = 1
epsilon_rf = inf
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
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 = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 2
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: 3.92594e+06
ref_t: 0
tau_t: 0
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0 0
energygrp_flags[ 1]: 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
On Fri, Feb 19, 2010 at 3:46 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
>
>
> ----- Original Message -----
> From: Amit Choubey <kgp.a...@gmail.com>
> Date: Saturday, February 20, 2010 10:25
> Subject: Re: [gmx-users] domain decomposition and load balancing
> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>
> > Hi Mark and Justin,
> > I am using a box of size (20nm)x(20nm)x(60nm)..system is open along z ie
> (60nm) side.>
> > I tried using only two nodes, it gives the same error>
>
> > There is no domain decomposition for 2 nodes that is compatible with the
> given box and a minimum cell size of 0.889862 nm> Change the number of nodes
> or mdrun option -rdd or -dds> Look in the log file for details on the domain
> decomposition
>
> ... so what does the log file say?
>
> Mark
>
> > On Fri, Feb 19, 2010 at 3:16 PM, Mark Abraham <mark.abra...@anu.edu.au>
> wrote:
>
> > ----- Original Message -----
> >
> From: "Justin A. Lemkul" <jalem...@vt.edu>
> >
> Date: Saturday, February 20, 2010 10:13
> >
> Subject: Re: [gmx-users] domain decomposition and load balancing
> >
> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>
> >
> >
> >
> >
> >
>
> > > Amit Choubey wrote:
> >
> > >Hi Mark,
> >
> > >
> >
> > >I am not using PME calculation.
> >
> > >
> >
> > >I was hoping mdrun will do the cell allocation itself.
> >
> > >
> >
> >
> >
> > It will, unless it can't, which is exactly your problem.
> >
> > Mark's point stands, regardless of whether or not you're using
> >
> > PME. DD requires certain minimum size requirements (which
> >
> > are discussed in the manual and the Gromacs 4 paper), so you
> >
> > have two choices:
> >
> >
> >
> > 1. Read about the options mdrun is telling you about.
> >
> > 2. Use fewer nodes so that the DD algorithm can construct
> >
> > reasonably-sized domains.
>
> >
>
> > 3. Use a larger simulation system so the minimum cell size is larger
> w.r.t. the cutoffs
> >
> 4. (If reasonable) Don't use pbc=xy
>
> >
> >
> Mark
> >
> --
> >
> gmx-users mailing list gmx-users@gromacs.org
>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >
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> >
>
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