[gmx-users] MDRUN crash
Luca Banetta
luca.banetta at gmail.com
Fri Jun 17 08:43:37 CEST 2016
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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