[gmx-users] mdrun crash

[Justin Lemkul]

On 2/23/15 12:12 AM, rahul dhakne wrote:
> Dear Gromacs user,
>
> I am running mdrun to minimize (energy minimization) my structure
> co-ordinate, but every time it stuck by displaying following error
>>>>>>>>>>>>
>   Back Off! I just backed up em.log to ./#em.log.8#
> Reading file em.tpr, VERSION 5.0.4 (single precision)
> Using 1 MPI thread
> Using 16 OpenMP threads
>
> 1 GPU detected:
>    #0: NVIDIA Quadro K600, compute cap.: 3.0, ECC:  no, stat: compatible
>
> 1 GPU auto-selected for this run.
> Mapping of GPU to the 1 PP rank in this node: #0
>
> Setting the maximum number of constraint warnings to -1
>
> Back Off! I just backed up em.trr to ./#em.trr.8#
>
> Back Off! I just backed up em.edr to ./#em.edr.8#
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+01
>     Number of steps    =        50000
>
> WARNING: Listed nonbonded interaction between particles 51227 and 51230
> at distance 8.421 which is larger than the table limit 2.000 nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
>
>
> step=       0, Dmax= 1.0e-02 nm, Epot=          nan Fmax= 2.79093e+14,
> atom= 39526
>
>>>>>
> Parameter file is following
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 10   ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
> emstep      = 0.01      ; Energy step size
> nsteps = 50000   ; Maximum number of (minimization) steps to perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist    = 1.4    ; Frequency to update the neighbor list and long range

nstlist needs an integer value.

> forces
> cutoff-scheme   = Verlet
> ns_type    = grid ; Method to determine neighbor list (simple, grid)
> coulombtype    = PME ; Treatment of long range electrostatic interactions
> rcoulomb    = 1.0 ; Short-range electrostatic cut-off
> rvdw    = 1.0 ; Short-range Van der Waals cut-off
> pbc        = xyz ; Periodic Boundary Conditions (yes/no)
> constraints     = none
>>>>>>>>
>
> Please provide the solution to fix this error.
>

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-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

==================================================