[gmx-users] a fatal error in step mdrun -v -deffnm em &

[Justin Lemkul]

On 3/30/16 8:36 AM, Brett wrote:
> Dear All,
>
> After steps for  pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c target_solv_ions.gro -p topol.top -o em.tpr", I started step "mdrun -v -deffnm em &", but in the "mdrun -v -deffnm em &" step it gave
>
> "Step=   15, Dmax= 1.3e-01 nm, Epot= -4.22195e+07 Fmax= 7.18492e+04, atom= 7837
> Step=   16, Dmax= 1.5e-01 nm, Epot= -4.23771e+07 Fmax= 1.46229e+05, atom= 5656
> Step=   17, Dmax= 1.8e-01 nm, Epot= -4.24412e+07 Fmax= 7.58589e+05, atom= 5656
>
> Back Off! I just backed up step18b_n8.pdb to ./#step18b_n8.pdb.1#
>
> Back Off! I just backed up step18c_n8.pdb to ./#step18c_n8.pdb.1#
> Wrote pdb files with previous and current coordinates
>
> -------------------------------------------------------
> Program gmx mdrun, VERSION 5.1.2
> Source code file: /home/FANFENGHUI/Desktop/WORK2016_2/GROMACS/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555
>
> Fatal error:
>
> step 18: Water molecule starting at atom 964420 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> "
>
> My minim.mdp was as following,
>
> "; ions.mdp - used as input into grompp to generate ions.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator  = steep     ; Algorithm (steep = steepest descent minimization)
> emtol       = 500.0    ; 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         ; Frequency to update the neighbor list and long range forces
> cutoff-scheme = Verlet
> ns_type     = grid      ; Method to determine neighbor list (simple, grid)
> coulombtype = PME       ; Treatment of long range electrostatic interactions
> rcoulomb    = 1.4       ; Short-range electrostatic cut-off
> rvdw        = 1.4       ; Short-range Van der Waals cut-off
> pbc         = xyz       ; Periodic Boundary Conditions"
>
> Will you please let me know why the fatal error in step 18 occurred, and how to avid it?
>

Look at the atom that the error message complains about, as well as the atom on 
which Fmax is acting, for an indication of the source of the problem. 
Typically, if EM fails, either your coordinates are unreasonable or your 
topology is broken.

-Justin

-- 
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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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