[gmx-users] MDRUN crash
Luca Banetta
luca.banetta at gmail.com
Fri Jun 17 09:56:29 CEST 2016
Thank you for your support mark! I run an equilibration with a simple
acetone molecule and it works with the mdp file i wrote in the first
e-mail. I try to take a look at the shell to see if i made mistakes in its
definition.
Il 17/Giu/2016 08:47, "Mark Abraham" <mark.j.abraham at gmail.com> ha scritto:
> Hi,
>
> Please don't start new work with old out-of-maintenance software, or at
> least use the most recent bug fix from that release branch. You should also
> do an equilibration with a normal acetone first, so that you know whether
> it's your equilibration or your shell model that is the problem.
>
> Mark
>
> On Fri, Jun 17, 2016 at 8:44 AM Luca Banetta <luca.banetta at gmail.com>
> wrote:
>
> > thank you for the advice justin! i have made some research and i use PME
> > for electrostatics that i noticed it's pretty common. Unfortunately the
> > mdrun this fatal error appeared:
> > Program mdrun, VERSION 4.5.4
> > Source code file: pme.c, line: 538
> >
> > Fatal error:
> > 1629 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 x.
> > This usually means that your system is not well equilibrated.
> >
> >
> > For out simulation we created a topology for the acetone molecule using
> > opls-AA force field introudicing a shell particle inside the topology.
> > At the moment the simulation is based on a single acetone molecule
> inside a
> > "sea" of water.
> > [ moleculetype ]
> > ; Name nrexcl
> > acetone 3
> >
> > [ atoms ]
> > ; nr type resnr residue atom cgnr charge
> > mass typeB chargeB massB
> > 1 opls_280 1 LIG C 1 0.47
> > 12.011
> > 2 opls_135 1 LIG C 2 -0.18
> > 12.011
> > 3 opls_135 1 LIG C 3 -0.18
> > 12.011
> > 4 opls_281 1 LIG O 4 0.47
> > 15.5994
> > 5 opls_282 1 LIG H 5 0.06
> > 1.008
> > 6 opls_282 1 LIG H 6 0.06
> > 1.008
> > 7 opls_282 1 LIG H 7 0.06
> > 1.008
> > 8 opls_282 1 LIG H 8 0.06
> > 1.008
> > 9 opls_282 1 LIG H 9 0.06
> > 1.008
> > 10 opls_282 1 LIG H 10 0.06
> > 1.008
> > 11 VS 1 LIG VS 11
> > -0.47 0.000
> > 12 SP 1 LIG SP 12
> > -0.47 0.000
> >
> > [ bonds ]
> > ; ai aj funct c0 c1 c2 c3
> > 1 2 1
> > 1 3 1
> > 1 4 1
> > 4 11 6
> > 11 12 6
> > 2 5 1
> > 2 6 1
> > 2 7 1
> > 3 8 1
> > 3 9 1
> > 3 10 1
> >
> > [ pairs ]
> > ; ai aj funct c0 c1 c2 c3
> > 2 8 1
> > 2 9 1
> > 2 10 1
> > 3 5 1
> > 3 6 1
> > 3 7 1
> > 4 5 1
> > 4 6 1
> > 4 7 1
> > 4 8 1
> > 4 9 1
> > 4 10 1
> >
> > [ angles ]
> > ; ai aj ak funct c0 c1
> > c2 c3
> > 2 1 3 1
> > 2 1 4 1
> > 3 1 4 1
> > 1 2 5 1
> > 1 2 6 1
> > 1 2 7 1
> > 5 2 6 1
> > 5 2 7 1
> > 6 2 7 1
> > 1 3 8 1
> > 1 3 9 1
> > 1 3 10 1
> > 8 3 9 1
> > 8 3 10 1
> > 9 3 10 1
> >
> > [ dihedrals ]
> > ; ai aj ak al funct c0 c1
> > c2 c3 c4 c5
> > 3 1 2 5 3
> > 3 1 2 6 3
> > 3 1 2 7 3
> > 4 1 2 5 3
> > 4 1 2 6 3
> > 4 1 2 7 3
> > 2 1 3 8 3
> > 2 1 3 9 3
> > 2 1 3 10 3
> > 4 1 3 8 3
> > 4 1 3 9 3
> > 4 1 3 10 3
> >
> > [ virtual_sites2 ]
> > ; site ai aj funct a
> > 11 1 4 1 1.05
> >
> > VS and SP have been introduced in the "ffnonbonded" and "ffbonded"
> sections
> > in the library oplsaa.ff
> >
> > 2016-06-16 15:05 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
> >
> > >
> > >
> > > On 6/16/16 6:10 AM, Luca Banetta wrote:
> > >
> > >> Dear gmx users,
> > >> I am meeting a lot of problems launching a simulation with shell
> > >> particles.
> > >> The mdp file is
> > >> ; VARIOUS PREPROCESSING OPTIONS
> > >> title = Yo
> > >> cpp = /usr/bin/cpp
> > >> include =
> > >> define =
> > >>
> > >> ; RUN CONTROL PARAMETERS
> > >> integrator = md
> > >> ; Start time and timestep in ps
> > >> tinit = 0
> > >> dt = 0.001
> > >> nsteps = 1000000
> > >> ; For exact run continuation or redoing part of a run
> > >> init_step = 0
> > >> ; mode for center of mass motion removal
> > >> 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
> > >> ; Temperature, friction coefficient (amu/ps) and random seed
> > >> bd-temp = 300
> > >> bd-fric = 0
> > >> ld-seed = 1993
> > >>
> > >> ; ENERGY MINIMIZATION OPTIONS
> > >> ; Force tolerance and initial step-size
> > >> emtol = 100
> > >> emstep = 0.01
> > >> ; Max number of iterations in relax_shells
> > >> niter = 20
> > >> ; Step size (1/ps^2) for minimization of flexible constraints
> > >> fcstep = 0
> > >> ; Frequency of steepest descents steps when doing CG
> > >> nstcgsteep = 1000
> > >> nbfgscorr = 10
> > >>
> > >> ; OUTPUT CONTROL OPTIONS
> > >> ; Output frequency for coords (x), velocities (v) and forces (f)
> > >> nstxout =
> > >> nstvout =
> > >> nstfout =
> > >> ; Checkpointing helps you continue after crashes
> > >> nstcheckpoint = 1000
> > >> ; Output frequency for energies to log file and energy file
> > >> nstlog = 50
> > >> nstenergy = 50
> > >> ; Output frequency and precision for xtc file
> > >> nstxtcout = 50
> > >> 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 = 5
> > >> ; ns algorithm (simple or grid)
> > >> ns_type = grid
> > >> ; Periodic boundary conditions: xyz (default), no (vacuum)
> > >> ; or full (infinite systems only)
> > >> pbc = xyz
> > >> ; nblist cut-off
> > >> rlist = 0.9
> > >> domain-decomposition = no
> > >>
> > >> ; OPTIONS FOR ELECTROSTATICS AND VDW
> > >> ; Method for doing electrostatics
> > >> coulombtype = Cut-off
> > >> rcoulomb-switch = 0
> > >> rcoulomb = 0.9
> > >> ; Dielectric constant (DC) for cut-off or DC of reaction field
> > >> epsilon-r = 1
> > >> ; Method for doing Van der Waals
> > >> vdw-type = Cut-off
> > >> ; cut-off lengths
> > >> rvdw-switch = 0
> > >> rvdw = 0.9
> > >> ; Apply long range dispersion corrections for Energy and Pressure
> > >> DispCorr = EnerPres
> > >> ; Extension of the potential lookup tables beyond the cut-off
> > >> table-extension = 1
> > >> ; 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
> > >>
> > >> ; 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
> > >> ; Salt concentration in M for Generalized Born models
> > >> gb_saltconc = 0
> > >>
> > >> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> > >> implicit_solvent = No
> > >>
> > >> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> > >> ; Temperature coupling
> > >> Tcoupl = berendsen
> > >> ; Groups to couple separately
> > >> tc-grps = System
> > >> ; Time constant (ps) and reference temperature (K)
> > >> tau_t = 0.1
> > >> ref_t = 300
> > >> ; Pressure coupling
> > >> Pcoupl = berendsen
> > >> Pcoupltype = isotropic
> > >> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> > >> tau_p = 1.0
> > >> compressibility = 4.5e-5
> > >> ref_p = 1.0
> > >> ; Random seed for Andersen thermostat
> > >> andersen_seed = 815131
> > >>
> > >> ; SIMULATED ANNEALING
> > >> ; Type of annealing for each temperature group (no/single/periodic)
> > >> annealing = no
> > >> ; 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 = 300
> > >> gen_seed = 1993
> > >>
> > >> ; OPTIONS FOR BONDS
> > >> constraints = all-bonds
> > >> ; Type of constraint algorithm
> > >> constraint-algorithm = Lincs
> > >> ; Do not constrain the start configuration
> > >> unconstrained-start = 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 =
> > >>
> > >> ; 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) to energy file
> > >> nstorireout = 100
> > >> ; Dihedral angle restraints: No, Simple or Ensemble
> > >> dihre = No
> > >> dihre-fc = 1000
> > >> dihre-tau = 0
> > >> ; Output frequency for dihedral values to energy file
> > >> nstdihreout = 100
> > >>
> > >> ; Free energy control stuff
> > >> free-energy = no
> > >> init-lambda = 0
> > >> delta-lambda = 0
> > >> sc-alpha = 0
> > >> sc-sigma = 0.3
> > >>
> > >> ; Non-equilibrium MD stuff
> > >> acc-grps =
> > >> accelerate =
> > >> freezegrps =
> > >> freezedim =
> > >> cos-acceleration = 0
> > >>
> > >> ; 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
> > >>
> > >>
> > >> In the log file it is written that RMS force on the shell is -nan and
> > it
> > >> can't do EM.
> > >> Can someone give me some advice in order to make EM possible?
> > >>
> > >
> > > Please provide full details about what the system is and how you built
> > > it. Also note that using plain cutoff electrostatics went out of style
> > > about 20 years ago as it is horribly inaccurate.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > 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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