[gmx-users] mdrun error
Justin Lemkul
jalemkul at vt.edu
Mon May 19 23:21:35 CEST 2014
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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>>
>
>
>
--
==================================================
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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