[gmx-users] mdrun error
Lovika Moudgil
lovikamoudgil at gmail.com
Tue May 20 08:39:29 CEST 2014
Thanks for help Justin.
Regards
Lovika
On Tue, May 20, 2014 at 2:49 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/19/14, 11:24 AM, Lovika Moudgil wrote:
>
>> 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....
>>
>>
> Something is inconsistent; your error message says rlist is 1.8, but your
> .mdp says it is 1.0.
>
> Regardless, either you have some very nasty charge groups (way too large)
> or you simply have groups broken across PBC, which is not actually a
> problem. Recent versions of grompp are smart enough to deal with PBC, so
> this would only show up with an old version of Gromacs.
>
> http://www.gromacs.org/Documentation/Errors#The_sum_
> of_the_two_largest_charge_group_radii_(X)_is_larger_
> than.c2.a0rlist_-_rvdw.2frcoulomb
>
> -Justin
>
> ; 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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>>>>>>> posting!
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>>>>>> --
>>>>> Gromacs Users mailing list
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>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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