[gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off
Subramaniam Boopathi
boopathiphd at gmail.com
Fri Feb 8 07:48:52 CET 2013
dear sir,
how can i remove this following problem
Log file opened on Fri Feb 8 12:04:27 2013
Host: alzhimer pid: 3977 nodeid: 0 nnodes: 1
The Gromacs distribution was built Mon Dec 3 10:09:10 IST 2012 by
root at alzhimer (Linux 2.6.32-279.el6.x86_64 x86_64)
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) ./mdrun_d (double precision) (-:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------
Input Parameters:
integrator = md
nsteps = 50000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 10
comm_mode = Linear
nstlog = 10
nstxout = 500
nstvout = 5000
nstfout = 0
nstcalcenergy = 10
nstenergy = 50
nstxtcout = 500
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 32
nky = 32
nkz = 32
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 = V-rescale
nsttcouple = 10
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 = 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: 248.91 8028.09
ref_t: 300 300
tau_t: 0.1 0.1
anneal: No No
ann_npoints: 0 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
Initializing Domain Decomposition on 12 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.396 nm, LJ-14, atoms 5 13
multi-body bonded interactions: 0.396 nm, Proper Dih., atoms 5 13
Minimum cell size due to bonded interactions: 0.436 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.763 nm
Estimated maximum distance required for P-LINCS: 0.763 nm
This distance will limit the DD cell size, you can override this with -rcon
Guess for relative PME load: 0.30
Will use 8 particle-particle and 4 PME only nodes
This is a guess, check the performance at the end of the log file
Using 4 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 0.953 nm
The maximum allowed number of cells is: X 3 Y 3 Z 3
Domain decomposition grid 2 x 2 x 2, separate PME nodes 4
PME domain decomposition: 2 x 2 x 1
Interleaving PP and PME nodes
This is a particle-particle only node
Domain decomposition nodeid 0, coordinates 0 0 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. Essmann, L. Perera, 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
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
System total charge: -0.102
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
Generated table with 4000 data points for 1-4 COUL.
Tabscale = 2000 points/nm
Generated table with 4000 data points for 1-4 LJ6.
Tabscale = 2000 points/nm
Generated table with 4000 data points for 1-4 LJ12.
Tabscale = 2000 points/nm
Enabling SPC-like water optimization for 1330 molecules.
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing x86_64 SSE2 support... present.
Removing pbc first time
Initializing Parallel LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
-------- -------- --- Thank You --- -------- --------
The number of constraints is 153
There are inter charge-group constraints,
will communicate selected coordinates each lincs iteration
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
Linking all bonded interactions to atoms
There are 817 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: X 1 Y 1 Z 1
The initial domain decomposition cell size is: X 1.60 nm Y 1.56 nm Z 1.56 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.000 nm
two-body bonded interactions (-rdd) 1.000 nm
multi-body bonded interactions (-rdd) 1.000 nm
atoms separated by up to 5 constraints (-rcon) 1.562 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1 Z 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 0.62 Y 0.64 Z 0.64
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.000 nm
two-body bonded interactions (-rdd) 1.000 nm
multi-body bonded interactions (-rdd) 1.000 nm
atoms separated by up to 5 constraints (-rcon) 1.000 nm
Making 3D domain decomposition grid 2 x 2 x 2, home cell index 0 0 0
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------
There are: 4141 Atoms
Charge group distribution at step 0: 176 171 197 177 196 201 171 192
Grid: 6 x 6 x 4 cells
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 5.99e-05
Initial temperature: 303.698 K
Started mdrun on node 0 Fri Feb 8 12:04:27 2013
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
2.36059e+03 3.53976e+02 7.34586e+00 7.00084e+03 2.02621e+03
LJ (SR) Coulomb (SR) Coul. recip. Position Rest. Potential
7.70414e+03 -5.91044e+04 -6.76092e+03 1.80260e+00 -4.64104e+04
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
6.48550e+04 1.84446e+04 1.84446e+04 1.88479e+03 7.32453e+03
Constr. rmsd
4.81184e-01
-------------------------------------------------------
Program mdrun_d, VERSION 4.5.5
Source code file: pme.c, line: 538
Fatal error:
1 particles communicated to PME node 0 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"As Always Your Logic Is Impeccable" (Tuvok)
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