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

[Brett]

gmx genion -s ions.tpr -o target_solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.15








At 2016-03-30 21:38:49, "SAKO MIRZAIE" <sako.biochem at gmail.com> wrote:
>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
>>
>>
>> --
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>
>
>-- 
>***********************************************
>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/
>-- 
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