[gmx-users] MDRUN crash
Justin Lemkul
jalemkul at vt.edu
Thu Jun 16 15:06:14 CEST 2016
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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