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

[SAKO MIRZAIE]

let me see your neutralizing command to produce ions.tpr.

On 3/30/16, Brett <brettliu123 at 163.com> 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?
>
> Based on "Step=   16, Dmax= 1.5e-01 nm, Epot= -4.23771e+07 Fmax=
> 1.46229e+05, atom= 5656", does it mean that step only works on atop "5656"?
> If so, if my system contains 500,000 atoms, how much should be the
> appropriate value for "nsteps" in the minim.mdp file?
>
> Brett
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-request at gromacs.org.
>


-- 
***********************************************
sako mirzaie
PhD in biochemistry, science faculty, Islamic azad university of
sanandaj, sanandaj, Iran
http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie

http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie

http://scholar.google.com/citations?user=viwZvVAAAAAJ&hl=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/