[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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