[gmx-users] mdrun running without simulating new steps
st
y1gao at ucsd.edu
Wed Sep 2 00:58:07 CEST 2009
Hi,
I run a two-molecule system with mdrun_d in a water box (~10000 water molecules.)
The program looks running properly (no errors nor warnnings)
However the program seems stop outputting files (because the output file size stop increases) after about 5min.
The mdrun_d interface looks normal without any errors, the md.log contains only two saves:
Any help/suggestions will be greatly appreciated!
Thank you!!
Stone Gao
**********************
Input Parameters:
integrator = md
nsteps = 40000
init_step = 0
ns_type = Grid
nstlist = 1
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 100
nstenergy = 100
nstxtcout = 100
init_t = 0
delta_t = 0.0005
xtcprec = 1e+06
nkx = 60
nky = 60
nkz = 90
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = Nose-Hoover
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
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 = 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 = 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: 96048
ref_t: 300
tau_t: 0.5
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
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
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 --- -------- --------
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
System total charge: -20.000
Generated table with 4000 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 4000 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 4000 data points for LJ12.
Tabscale = 2000 points/nm
Enabling SPC water optimization for 10139 molecules.
Configuring nonbonded kernels...
Testing ia32 SSE2 support... present.
Removing pbc first time
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 32017 Atoms
Max number of connections per atom is 37
Total number of connections is 102233
Max number of graph edges per atom is 4
Total number of graph edges is 44156
Initial temperature: 0 K
Started mdrun on node 0 Tue Sep 1 15:25:43 2009
Step Time Lambda
0 0.00000 0.00000
Grid: 9 x 9 x 14 cells
Energies (kJ/mol)
Bond Morse Angle G96Angle Proper Dih.
3.35232e+05 3.27635e+01 7.09937e+02 1.73811e+01 2.47097e+03
LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
1.48669e+05 -4.50390e+05 -1.89304e+04 1.78117e+04 4.38796e+05
Total Energy Conserved En. Temperature Pressure (bar)
4.56608e+05 4.56608e+05 1.09892e+03 -5.74950e+04
Step Time Lambda
100 0.05000 0.00000
Energies (kJ/mol)
Bond Morse Angle G96Angle Proper Dih.
3.38536e+05 1.06967e+03 2.21584e+04 4.26526e+01 3.13457e+03
LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
8.73487e+04 -5.64854e+05 -4.48577e+04 -1.57422e+05 3.56524e+05
Total Energy Conserved En. Temperature Pressure (bar)
1.99102e+05 7.60608e+05 8.92881e+02 7.56563e+04
**********************
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