[gmx-users] mdrun crash when -np 8, not when -np 4
Malcolm Gillies
malcolm.b.gillies at anu.edu.au
Fri Aug 22 04:36:01 CEST 2003
I have an mdrun job which crashes when I attempt to run it over 8
processors, but which appears to run fine with 4 processors. Any
suggestions?
I'm running Gromacs 3.1.4 on Alpha system. The mdp file and log files
are attached (I'm using PME).
The stack trace on crash:
prun: /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi (pid 13747743) killed by signal 11 (SIGSEGV)
prun: generating backtrace for /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi /local/core/rms/291775/core.mdrun_mpi.sc89.0
Welcome to the Ladebug Debugger Version 67 (built Mar 10 2002 for Compaq Tru64 UNIX)
------------------
object file name: /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
core file name: /local/core/rms/291775/core.mdrun_mpi.sc89.0
Reading symbolic information ...done
Core file produced from executable 'mdrun_mpi'
Thread 8 terminated at PC 0x12010c120 by signal SEGV
Stack trace for thread 8
>0 0x12010c120 in angles(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#1 0x12010ab70 in calc_bonds(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#2 0x1200915d0 in force(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#3 0x120081240 in do_force(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#4 0x12007af54 in do_md(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#5 0x120079b9c in mdrunner(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#6 0x12007cad0 in main(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#7 0x12006aed8 in __start(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
Stack trace for thread 7
#0 0x3ff801374e8 in __syscall(...) in /usr/shlib/libc.so
#1 0x300010195c0 in elan3_syscall_lwp(ctx=Info: no allocation applies for symbol ctx at the current PC
<no value>) "syscall_dunix.c":201
#2 0x30001007ff8 in elan3_lwp(arg=0x140022800) "elanlib.c":85
prun: dumping elan exception state for /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi /local/core/rms/291775/core.mdrun_mpi.sc89.0
edb: found exception list at 4102bde0
edb: exceptions from '/opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi'
prun:
cheers,
Malcolm
--
Malcolm Gillies <Malcolm.B.Gillies at anu.edu.au>
Postdoctoral Fellow, Computational Proteomics and Therapy Design Group,
John Curtin School of Medical Research, Australian National University
-------------- next part --------------
title = MD
cpp = /lib/cpp
constraints = hbonds
integrator = md
dt = 0.001 ; ps !
nsteps = 1000000 ; total 500 ps.
nstcomm = 1
nstxout = 10000
nstvout = 10000
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
coulombtype = PME
rcoulomb_switch = 0.0
dispcorr = EnerPres
epsilon_surface = 78.0
fourierspacing = 0.1
pmeorder = 6
optimizefft = no
; Nose-Hoover coupling is on in two groups
Tcoupl = Nose-Hoover
tau_t = 0.1 0.1
tc-grps = protein sol
ref_t = 300 300
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
-------------- next part --------------
Log file opened: nodeid 0, nnodes = 8, host = unknown, process = 13747743
:-) G R O M A C S (-:
GROningen MAchine for Chemical Simulation
:-) VERSION 3.1.4 (-:
Copyright (c) 1991-2002, University of Groningen, The Netherlands
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_mpi (-:
++++++++ PLEASE 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 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 --- -------- --------
CPU= 0, lastcg= 4371, targetcg=21620, myshift= 5
CPU= 1, lastcg= 8677, targetcg=25926, myshift= 5
CPU= 2, lastcg=12980, targetcg=30229, myshift= 5
CPU= 3, lastcg=17283, targetcg= 35, myshift= 5
CPU= 4, lastcg=21586, targetcg= 4338, myshift= 4
CPU= 5, lastcg=25889, targetcg= 8641, myshift= 4
CPU= 6, lastcg=30193, targetcg=12945, myshift= 4
CPU= 7, lastcg=34496, targetcg=17248, myshift= 4
nsb->shift = 5, nsb->bshift= 0
Listing Scalars
nsb->nodeid: 0
nsb->nnodes: 8
nsb->cgtotal: 34497
nsb->natoms: 103277
nsb->shift: 5
nsb->bshift: 0
Nodeid index homenr cgload workload
0 0 12910 4372 4372
1 12910 12910 8678 8678
2 25820 12909 12981 12981
3 38729 12909 17284 17284
4 51638 12909 21587 21587
5 64547 12909 25890 25890
6 77456 12912 30194 30194
7 90368 12909 34497 34497
parameters of the run (nodeid=0):
input record:
integrator = md
nsteps = 1000000
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
nstlog = 100
nstxout = 10000
nstvout = 10000
nstfout = 0
nstenergy = 100
nstxtcout = 0
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 96
nky = 112
nkz = 104
pme_order = 6
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 78
optimize_fft = FALSE
ePBC = xyz
bUncStart = FALSE
bShakeSOR = FALSE
etc = Nose-Hoover
epc = Parrinello-Rahman
epctype = Isotropic
tau_p = 0.5
ref_p (3x3):
ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
compress (3x3):
compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
bSimAnn = FALSE
zero_temp_time = 0
rlist = 1.2
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.2
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.2
epsilon_r = 1
DispCorr = EnerPres
fudgeQQ = 0.5
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
em_stepsize = 0.01
em_tol = 100
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
ConstAlg = Lincs
shake_tol = 0.0001
lincs_order = 4
lincs_warnangle = 30
bd_temp = 300
bd_fric = 0
ld_seed = 1993
cos_accel = 0
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 42165.4 172852
ref_t: 300 300
tau_t: 0.1 0.1
acc: 0 0 0
nfreeze: N N N
energygrp_excl[ 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
box (3x3):
box[ 0]={ 9.05361e+00, 0.00000e+00, 0.00000e+00}
box[ 1]={ 0.00000e+00, 1.08158e+01, 0.00000e+00}
box[ 2]={ 0.00000e+00, 0.00000e+00, 1.01414e+01}
ekin (3x3):
ekin[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ekin[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ekin[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
pres (3x3):
pres[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
pres[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
pres[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
vir (3x3):
vir[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
vir[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
vir[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 4
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Will do PME sum in reciprocal space.
++++++++ PLEASE 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 --- -------- --------
Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
local_nx: 12 local_x_start: 0
local_ny_after_transpose: 14 local_y_start_after_transpose 0
total_local_size: 142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 639645
There are: 12910 Atom
Removing pbc first time
Done rmpbc
Constraining the starting coordinates (step -2)
++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
Initializing LINear Constraint Solver
number of constraints is 6446
average number of constraints coupled to one constraint is 0.9
-------------- next part --------------
Log file opened: nodeid 1, nnodes = 8, host = unknown, process = 13747744
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 4
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 1
There are 2990 optimized water molecules on node 1
Will do PME sum in reciprocal space.
++++++++ PLEASE 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 --- -------- --------
Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
local_nx: 12 local_x_start: 12
local_ny_after_transpose: 14 local_y_start_after_transpose 14
total_local_size: 142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 639645
There are: 12910 Atom
Removing pbc first time
Done rmpbc
Constraining the starting coordinates (step -2)
++++++++ PLEASE 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 --- -------- --------
++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
Initializing LINear Constraint Solver
number of constraints is 1938
average number of constraints coupled to one constraint is 0.9
-------------- next part --------------
Log file opened: nodeid 2, nnodes = 8, host = unknown, process = 13747741
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 2
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 2
There are 4303 optimized water molecules on node 2
Will do PME sum in reciprocal space.
++++++++ PLEASE 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 --- -------- --------
Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
local_nx: 12 local_x_start: 24
local_ny_after_transpose: 14 local_y_start_after_transpose 28
total_local_size: 142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 639645
There are: 12909 Atom
Removing pbc first time
Done rmpbc
Constraining the starting coordinates (step -2)
++++++++ PLEASE 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 --- -------- --------
-------------- next part --------------
Log file opened: nodeid 3, nnodes = 8, host = unknown, process = 13747747
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 2
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 3
There are 4303 optimized water molecules on node 3
Will do PME sum in reciprocal space.
++++++++ PLEASE 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 --- -------- --------
Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
local_nx: 12 local_x_start: 36
local_ny_after_transpose: 14 local_y_start_after_transpose 42
total_local_size: 142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 639645
There are: 12909 Atom
Removing pbc first time
Done rmpbc
Constraining the starting coordinates (step -2)
++++++++ PLEASE 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 --- -------- --------
-------------- next part --------------
Log file opened: nodeid 4, nnodes = 8, host = unknown, process = 14744071
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 2
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 4
There are 4303 optimized water molecules on node 4
Will do PME sum in reciprocal space.
++++++++ PLEASE 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 --- -------- --------
Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
local_nx: 12 local_x_start: 48
local_ny_after_transpose: 14 local_y_start_after_transpose 56
total_local_size: 142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 639645
There are: 12909 Atom
Removing pbc first time
Done rmpbc
Constraining the starting coordinates (step -2)
++++++++ PLEASE 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 --- -------- --------
-------------- next part --------------
Log file opened: nodeid 5, nnodes = 8, host = unknown, process = 14744072
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 2
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 5
There are 4303 optimized water molecules on node 5
Will do PME sum in reciprocal space.
++++++++ PLEASE 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 --- -------- --------
Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
local_nx: 12 local_x_start: 60
local_ny_after_transpose: 14 local_y_start_after_transpose 70
total_local_size: 142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 639645
There are: 12909 Atom
Removing pbc first time
Done rmpbc
Constraining the starting coordinates (step -2)
++++++++ PLEASE 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 --- -------- --------
-------------- next part --------------
Log file opened: nodeid 6, nnodes = 8, host = unknown, process = 14744073
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 2
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 6
There are 4304 optimized water molecules on node 6
Will do PME sum in reciprocal space.
++++++++ PLEASE 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 --- -------- --------
Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
local_nx: 12 local_x_start: 72
local_ny_after_transpose: 14 local_y_start_after_transpose 84
total_local_size: 142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 639645
There are: 12912 Atom
Removing pbc first time
Done rmpbc
Constraining the starting coordinates (step -2)
++++++++ PLEASE 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 --- -------- --------
-------------- next part --------------
Log file opened: nodeid 7, nnodes = 8, host = unknown, process = 14744074
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 2
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 7
There are 4303 optimized water molecules on node 7
Will do PME sum in reciprocal space.
++++++++ PLEASE 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 --- -------- --------
Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
local_nx: 12 local_x_start: 84
local_ny_after_transpose: 14 local_y_start_after_transpose 98
total_local_size: 142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 639645
There are: 12909 Atom
Removing pbc first time
Done rmpbc
Constraining the starting coordinates (step -2)
++++++++ PLEASE 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 --- -------- --------
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