[gmx-users] what does it mean by 'started mdrun on node 0'
Yihua Zhou
yihuaz0702 at gmail.com
Thu Nov 29 06:02:11 CET 2012
Dear Sir
I am very sorry to interrupt you again, but now I came across some problem
haven't checked out what was going wrong. I used Matlab to established the
DNA and graphene nanosheet model including all the .gro files, .itp files
and .top files. When I ran it, the computer didn't send out error
information, but it just has no calculations,below is the log file, could
you please take a look for me and provide some suggestion? I would really
appreciate your kindly help, looking forward to your reply.
Input Parameters:
integrator = sd
nsteps = 20000000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 0
comm_mode = None
nstlog = 100000
nstxout = 100000
nstvout = 100000
nstfout = 100000
nstcalcenergy = 10
nstenergy = 100000
nstxtcout = 100000
init_t = 0
delta_t = 0.01
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 = 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 = 0.9
rlistlong = 0.9
rtpi = 0.05
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 0.9
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 0.9
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 = 10
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: 33
ref_t: 300
tau_t: 0.05
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: Y Y Y Y Y
Y N N N
energygrp_flags[ 0]: 0 0
energygrp_flags[ 1]: 0 1
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
Initializing Domain Decomposition on 3 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Minimum cell size due to bonded interactions: 1.000 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 3 cells with a minimum initial size of 1.250 nm
The maximum allowed number of cells is: X 6 Y 3 Z 1
Domain decomposition grid 3 x 1 x 1, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 0.9
System total charge: -16.000
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing ia32 SSE2 support... present.
Removing pbc first time
Linking all bonded interactions to atoms
The initial number of communication pulses is: X 1
The initial domain decomposition cell size is: X 2.67 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 0.900 nm
two-body bonded interactions (-rdd) 1.000 nm
multi-body bonded interactions (-rdd) 1.000 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1
The minimum size for domain decomposition cells is 1.000 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.38
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 0.900 nm
two-body bonded interactions (-rdd) 1.000 nm
multi-body bonded interactions (-rdd) 1.000 nm
Making 1D domain decomposition grid 3 x 1 x 1, home cell index 0 0 0
There are: 301 Atoms
Charge group distribution at step 0: 115 98 88
Grid: 5 x 4 x 2 cells
Initial temperature: 306.651 K
Started mdrun on node 0 Wed Nov 28 23:02:33 2012
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond G96Angle Proper Dih. LJ (SR) Coulomb (SR)
4.19801e+05 1.40206e+03 3.49599e+03 8.36580e+20 8.17307e+04
Potential Kinetic En. Total Energy Temperature Pressure (bar)
8.36580e+20 inf inf inf inf
Best regards
Rita Zhou
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