[gmx-users] mdrun error
Lovika Moudgil
lovikamoudgil at gmail.com
Mon May 19 17:24:44 CEST 2014
Hiii Everyone....
I need some help....As in my grompp command I am getting warning about
charge group and rlist ....
Can any body help me to understand this ...
Warning is
WARNING 2 [file gro.mdp]:
The sum of the two largest charge group radii (5.930022) is larger than
rlist (1.800000)
and my .mdp file is....
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include =
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 0
; 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
; number of steps for center of mass motion removal
nstcomm = 10
; 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 = 100
nstvout = 100
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 100
nstcalcenergy = -1
nstenergy = 100
; Output frequency and precision for .xtc file
nstxtcout = 0
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 =
; 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
; long-range cut-off for switched potentials
rlistlong = -1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Cut-off
rcoulomb-switch = 0
rcoulomb = 1
; 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
; 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 = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; 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 = 1
; 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 = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension = -1
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = No
nsttcouple = -1
nh-chain-length = 10
; Groups to couple separately
tc-grps =
; Time constant (ps) and reference temperature (K)
tau-t =
ref-t =
; Pressure coupling
Pcoupl = No
Pcoupltype = Isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1
compressibility =
ref-p =
; 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 = no
gen-temp = 300
gen-seed = 173529
; OPTIONS FOR BONDS
constraints = none
; 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 = 0.0001
; 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 = no
; 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
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_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
Please guide me ......
Regards and Thanks
Lovika
On Sun, May 18, 2014 at 9:54 AM, Lovika Moudgil <lovikamoudgil at gmail.com>wrote:
> Mark thanks for your reply and support . [?]
>
> Regards
> Lovika
>
>
> On Sat, May 17, 2014 at 5:23 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> No, the .mdp file mostly describes your model physics (but there are some
>> implementation details that affect parallelization in there).
>>
>> Your GROMACS CMake configuration, mdrun command line and the attributes of
>> your hardware are the biggest factors that determine how mdrun will try to
>> parallelise. There's a lot of diagnostic reporting in the log file, but
>> you
>> are initially looking for the number of cells in the domain decomposition
>> (DD). And you need to know how big your simulation system is. For example,
>> a 900-molecule water system won't parallelise over a whole 32-core compute
>> server with a domain per core. Background info here
>> http://www.gromacs.org/Documentation/Acceleration_and_parallelization
>>
>> Mark
>>
>>
>> On Sat, May 17, 2014 at 9:02 AM, Lovika Moudgil <lovikamoudgil at gmail.com
>> >wrote:
>>
>> > Thanks for quick reply Mark...what information you are asking
>> for?Should I
>> > search for this my .mdp file??
>> >
>> > Thanks
>> > Lovika
>> >
>> >
>> > On Sat, May 17, 2014 at 11:35 AM, Mark Abraham <
>> mark.j.abraham at gmail.com
>> > >wrote:
>> >
>> > > Your simulation seems too small to parallelize in the way you/mdrun
>> > tried.
>> > > But we need more information to be sure.
>> > >
>> > > Mark
>> > > On May 17, 2014 7:33 AM, "Lovika Moudgil" <lovikamoudgil at gmail.com>
>> > wrote:
>> > >
>> > > > Hi Everyone ....
>> > > > I need some help. With my mdrun command I am getting this following
>> > error
>> > > > .
>> > > >
>> > > > Program mdrun, VERSION 4.6.5
>> > > > Source code file:
>> > > > /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c,
>> > line:
>> > > > 722
>> > > >
>> > > > Fatal error:
>> > > > DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connected
>> via
>> > > > constraints from the neighboring cells. This probably means your
>> > > constraint
>> > > > lengths are too long compared to the domain decomposition cell size.
>> > > > Decrease the number of domain decomposition grid cells or
>> lincs-order.
>> > > > For more information and tips for troubleshooting, please check the
>> > > GROMACS
>> > > > website at http://www.gromacs.org/Documentation/Errors
>> > > > -------------------------------------------------------
>> > > >
>> > > > Please help me to understand this error.What this error is all
>> about ?
>> > > > Where should I search to resolve this error ?
>> > > >
>> > > > Thanks
>> > > > Lovika
>> > > > --
>> > > > Gromacs Users mailing list
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