[gmx-users] v4.5b2 error specifically on 16 cores with npme 6
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Tue Aug 3 00:12:33 CEST 2010
Dear all:
I have an explicit solvent peptide-in-bilayer system taht also used
the pull-code.
This system runs fine on 8 cores in a single box with v4.0.7 and
4.5b2. It also runs fine on 16 cores IB for v4.0.7 but not 4.5b2. In
the later case, I get an exit from mdrun (see below). I have also
attached also the .mdp options. The strange thing is that I can the
system run fine on 56 cores IB.
In table form:
8 cores v4.0.7 ok
8 cores v4.5b2 ok
16 cores v4.0.7 ok
16 cores v4.5b2 <--- failure
56 cores v4.0.7 ok
56 cores v4.5b2 ok
############# 16 core division from log file
Using 6 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 10 cells with a minimum initial size of 0.964 nm
The maximum allowed number of cells is: X 4 Y 4 Z 11
Domain decomposition grid 1 x 2 x 5, separate PME nodes 6
PME domain decomposition: 1 x 6 x 1
Interleaving PP and PME nodes
This is a particle-particle only node
############# 56 core division from log file
Using 16 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 40 cells with a minimum initial size of 0.964 nm
The maximum allowed number of cells is: X 4 Y 4 Z 11
Domain decomposition grid 4 x 2 x 5, separate PME nodes 16
PME domain decomposition: 4 x 4 x 1
Interleaving PP and PME nodes
This is a particle-particle only node
I reproduced this crash.
I ran it again using -npme 0 ---> it ran fine.
I ran it again using -npme 4 ---> it ran fine.
I ran it again using -npme 6 ---> I got the same crash as previously
I thought about setting the pme grid divisions with something similar
to -dd but there does not appear to be such an option (listed via
mdrun -h, at least).
############ stderr from the 16 core failure
gpc-f101n084-$ cat jTEST.e2487310
Option Filename Type Description
------------------------------------------------------------
-f my.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c pbcmol.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n complete.ndx Input, Opt! Index file
-p this.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o md1.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input processing
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
NOTE 1 [file my.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file my.mdp]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
Generated 298378 of the 298378 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 298378 of the 298378 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'ANA'
Excluding 3 bonded neighbours molecule type 'DOPC'
Excluding 2 bonded neighbours molecule type 'SOL'
Setting gen_seed to 9385
Velocities were taken from a Maxwell distribution at 298 K
Pull group 0 'DOPC' has 3456 atoms
Pull group 1 'LEUJ' has 14 atoms
Number of degrees of freedom in T-Coupling group DOPC is 6975.39
Number of degrees of freedom in T-Coupling group SOL is 27327.61
Number of degrees of freedom in T-Coupling group LEUJ is 29.00
Pull group natoms pbc atom distance at start reference at t=0
0 3456 1742
1 14 7 -0.000 0.000 -0.001 0.000 0.000 0.000
Estimate for the relative computational load of the PME mesh part: 0.38
There were 2 notes
gcq#251: "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)
NNODES=16, MYRANK=0, HOSTNAME=gpc-f143n007
NNODES=16, MYRANK=2, HOSTNAME=gpc-f143n007
NNODES=16, MYRANK=7, HOSTNAME=gpc-f143n007
NNODES=16, MYRANK=1, HOSTNAME=gpc-f143n007
NNODES=16, MYRANK=5, HOSTNAME=gpc-f143n007
NNODES=16, MYRANK=6, HOSTNAME=gpc-f143n007
NNODES=16, MYRANK=3, HOSTNAME=gpc-f143n007
NNODES=16, MYRANK=4, HOSTNAME=gpc-f143n007
NNODES=16, MYRANK=14, HOSTNAME=gpc-f143n008
NNODES=16, MYRANK=10, HOSTNAME=gpc-f143n008
NNODES=16, MYRANK=12, HOSTNAME=gpc-f143n008
NNODES=16, MYRANK=15, HOSTNAME=gpc-f143n008
NNODES=16, MYRANK=11, HOSTNAME=gpc-f143n008
NNODES=16, MYRANK=9, HOSTNAME=gpc-f143n008
NNODES=16, MYRANK=13, HOSTNAME=gpc-f143n008
NNODES=16, MYRANK=8, HOSTNAME=gpc-f143n008
NODEID=5 argc=17
NODEID=13 argc=17
NODEID=4 argc=17
NODEID=12 argc=17
NODEID=0 argc=17
NODEID=8 argc=17
:-) G R O M A C S (-:
NODEID=2 argc=17
Green Red Orange Magenta Azure Cyan Skyblue
:-) VERSION 4.5-beta2 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
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.
NODEID=6 argc=17
:-)
/project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2/exec/bin/mdrun_openmpi-1.4.1
(-:
NODEID=11 argc=17
NODEID=14 argc=17
NODEID=15 argc=17
NODEID=10 argc=17
NODEID=9 argc=17
NODEID=7 argc=17
NODEID=1 argc=17
NODEID=3 argc=17
Option Filename Type Description
------------------------------------------------------------
-s md1.tpr Input Run input file: tpr tpb tpa
-o md1.trr Output Full precision trajectory: trr trj cpt
-x md1.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi md1.cpt Input, Opt! Checkpoint file
-cpo md1.cpt Output, Opt. Checkpoint file
-c md1.gro Output Structure file: gro g96 pdb etc.
-e md1.edr Output Energy file
-g md1.log Output Log file
-dhdl md1.xvg Output, Opt. xvgr/xmgr file
-field md1.xvg Output, Opt. xvgr/xmgr file
-table md1.xvg Input, Opt. xvgr/xmgr file
-tablep md1.xvg Input, Opt. xvgr/xmgr file
-tableb md1.xvg Input, Opt. xvgr/xmgr file
-rerun md1.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi md1.xvg Output, Opt. xvgr/xmgr file
-tpid md1.xvg Output, Opt. xvgr/xmgr file
-ei md1.edi Input, Opt. ED sampling input
-eo md1.edo Output, Opt. ED sampling output
-j md1.gct Input, Opt. General coupling stuff
-jo md1.gct Output, Opt. General coupling stuff
-ffout md1.xvg Output, Opt. xvgr/xmgr file
-devout md1.xvg Output, Opt. xvgr/xmgr file
-runav md1.xvg Output, Opt. xvgr/xmgr file
-px coord.xvg Output, Opt! xvgr/xmgr file
-pf force.xvg Output, Opt! xvgr/xmgr file
-mtx md1.mtx Output, Opt. Hessian matrix
-dn md1.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string md1 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum yes Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool no Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real 47.5 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Reading file md1.tpr, VERSION 4.5-beta2 (single precision)
Will use 10 particle-particle and 6 PME only nodes
This is a guess, check the performance at the end of the log file
Making 2D domain decomposition 1 x 2 x 5
starting mdrun 'Pure DOPC with 64 lipid molecules in 2807 water'
100000 steps, 200.0 ps.
-------------------------------------------------------
Program mdrun_openmpi-1.4.1, VERSION 4.5-beta2
Source code file: pme.c, line: 535
Fatal error:
522 particles communicated to PME node 1 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
-------------------------------------------------------
"Look at these, my work-strong arms" (P.J. Harvey)
Error on node 4, will try to stop all the nodes
Halting parallel program mdrun_openmpi-1.4.1 on CPU 4 out of 16
-------------------------------------------------------
Program mdrun_openmpi-1.4.1, VERSION 4.5-beta2
Source code file: pme.c, line: 535
Fatal error:
2667 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
-------------------------------------------------------
"Look at these, my work-strong arms" (P.J. Harvey)
Error on node 2, will try to stop all the nodes
Halting parallel program mdrun_openmpi-1.4.1 on CPU 2 out of 16
-------------------------------------------------------
Program mdrun_openmpi-1.4.1, VERSION 4.5-beta2
Source code file: pme.c, line: 535
Fatal error:
2734 particles communicated to PME node 2 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
-------------------------------------------------------
"Look at these, my work-strong arms" (P.J. Harvey)
Error on node 7, will try to stop all the nodes
Halting parallel program mdrun_openmpi-1.4.1 on CPU 7 out of 16
gcq#345: "Look at these, my work-strong arms" (P.J. Harvey)
gcq#345: "Look at these, my work-strong arms" (P.J. Harvey)
gcq#345: "Look at these, my work-strong arms" (P.J. Harvey)
-------------------------------------------------------
Program mdrun_openmpi-1.4.1, VERSION 4.5-beta2
Source code file: pme.c, line: 535
Fatal error:
478 particles communicated to PME node 4 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
-------------------------------------------------------
"Look at these, my work-strong arms" (P.J. Harvey)
Error on node 12, will try to stop all the nodes
Halting parallel program mdrun_openmpi-1.4.1 on CPU 12 out of 16
-------------------------------------------------------
Program mdrun_openmpi-1.4.1, VERSION 4.5-beta2
Source code file: pme.c, line: 535
Fatal error:
2540 particles communicated to PME node 5 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
-------------------------------------------------------
"Look at these, my work-strong arms" (P.J. Harvey)
Error on node 15, will try to stop all the nodes
Halting parallel program mdrun_openmpi-1.4.1 on CPU 15 out of 16
-------------------------------------------------------
Program mdrun_openmpi-1.4.1, VERSION 4.5-beta2
Source code file: pme.c, line: 535
Fatal error:
2622 particles communicated to PME node 3 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
-------------------------------------------------------
"Look at these, my work-strong arms" (P.J. Harvey)
Error on node 10, will try to stop all the nodes
Halting parallel program mdrun_openmpi-1.4.1 on CPU 10 out of 16
gcq#345: "Look at these, my work-strong arms" (P.J. Harvey)
gcq#345: "Look at these, my work-strong arms" (P.J. Harvey)
gcq#345: "Look at these, my work-strong arms" (P.J. Harvey)
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 10 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 12 with PID 8206 on
node gpc-f143n008 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[gpc-f143n007:09389] 5 more processes have sent help message
help-mpi-api.txt / mpi-abort
[gpc-f143n007:09389] Set MCA parameter "orte_base_help_aggregate" to 0
to see all help / error messages
###################### mdp file
gpc-f101n084-$ cat mdout.mdp
;
; File 'mdout.mdp' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Mon Aug 2 17:38:39 2010
;
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include =
; e.g.: -DI_Want_Cookies -DMe_Too
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 100000
; For exact run continuation or redoing part of a run
init_step = 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part = 1
; mode for center of mass motion removal
; energy calculation and T/P-coupling frequency
nstcalcenergy = -1
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 10000000
nstvout = 10000000
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 0
nstenergy = 5000
; Output frequency and precision for xtc file
nstxtcout = 5000
xtc-precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps = DOPC SOL LEUJ
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = no
; nblist cut-off
rlist = 1.0
; long-range cut-off for switched potentials
rlistlong = -1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = pme
rcoulomb-switch = 0
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
energygrp_table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 40
fourier_ny = 40
fourier_nz = 72
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = No
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension = 2.092
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = berendsen
nsttcouple = -1
nh-chain-length = 10
; Groups to couple separately
tc-grps = DOPC SOL LEUJ
; Time constant (ps) and reference temperature (K)
tau-t = 0.2 0.2 0.2
ref-t = 298 298 298
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = semi-isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1.0
compressibility = 4.5e-5 4.5e-5
ref-p = 1.0 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed = 815131
; OPTIONS FOR QMMM calculations
QMMM = no
; Groups treated Quantum Mechanically
QMMM-grps =
; QM method
QMmethod =
; QMMM scheme
QMMMscheme = normal
; QM basisset
QMbasis =
; QM charge
QMcharge =
; QM multiplicity
QMmult =
; Surface Hopping
SH =
; CAS space options
CASorbitals =
CASelectrons =
SAon =
SAoff =
SAsteps =
; Scale factor for MM charges
MMChargeScaleFactor = 1
; Optimization of QM subsystem
bOPT =
bTS =
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing =
; Number of time points to use for specifying annealing in each group
annealing_npoints =
; List of times at the annealing points for each group
annealing_time =
; Temp. at each annealing point, for each group.
annealing_temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen-temp = 298
gen-seed = -1
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
continuation = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl =
; WALLS
; Number of walls, type, atom types, densities and box-z scale factor
for Ewald
nwall = 0
wall_type = 9-3
wall_r_linpot = -1
wall_atomtype =
wall_density =
wall_ewald_zfac = 3
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry = position
; Select components for the pull vector. default: Y Y Y
pull_dim = N N Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1 = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0 = 1.5
pull_constr_tol = 1e-06
pull_start = no
pull_nstxout = 500
pull_nstfout = 500
; Number of pull groups
pull_ngroups = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)
pull_group0 = DOPC
pull_weights0 =
pull_pbcatom0 = 0
pull_group1 = LEUJ
pull_weights1 =
pull_pbcatom1 = 0
pull_vec1 = 0 0 0
pull_init1 = 0 0 0.0
pull_rate1 = 0
pull_k1 = 3000.0
pull_kB1 = 3000
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) and S to energy file
nstorireout = 100
; Dihedral angle restraints: No or Yes
dihre = no
dihre-fc = 1000
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
foreign_lambda =
sc-alpha = 0
sc-power = 0
sc-sigma = 0.3
nstdhdl = 10
dh_table_size = 0
dh_table_spacing = 0.1
couple-moltype =
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
gpc-f101n084-$
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