[gmx-users] simulation error

Tue Sep 18 17:55:38 CEST 2018

when i try to run mdrun they start showing this:
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Step=    0, Dmax= 1.0e-02 nm, Epot= -2.46652e+06 Fmax= 6.62812e+05, atom=
2881
Step=    1, Dmax= 1.0e-02 nm, Epot= -2.48761e+06 Fmax= 6.51531e+05, atom=
2881
Step=    2, Dmax= 1.2e-02 nm, Epot= -2.51019e+06 Fmax= 6.38455e+05, atom=
2881
Step=    3, Dmax= 1.4e-02 nm, Epot= -2.53494e+06 Fmax= 6.23418e+05, atom=
2881
Step=    4, Dmax= 1.7e-02 nm, Epot= -2.56238e+06 Fmax= 6.06180e+05, atom=
2881
Step=    5, Dmax= 2.1e-02 nm, Epot= -2.59295e+06 Fmax= 5.86164e+05, atom=
2881
Step=    6, Dmax= 2.5e-02 nm, Epot= -2.62704e+06 Fmax= 5.62063e+05, atom=
2881
Step=    7, Dmax= 3.0e-02 nm, Epot= -2.66494e+06 Fmax= 5.31531e+05, atom=
2881
Step=    8, Dmax= 3.6e-02 nm, Epot= -2.70684e+06 Fmax= 4.91124e+05, atom=
2881
Step=    9, Dmax= 4.3e-02 nm, Epot= -2.75366e+06 Fmax= 4.36752e+05, atom=
2881
Step=   10, Dmax= 5.2e-02 nm, Epot= -2.80104e+06 Fmax= 3.67647e+05, atom=
2881
Step=   11, Dmax= 6.2e-02 nm, Epot= -2.84787e+06 Fmax= 4.16988e+05, atom=
2883
Step=   12, Dmax= 7.4e-02 nm, Epot= -2.86654e+06 Fmax= 2.20175e+06, atom=
2903
Step=   13, Dmax= 8.9e-02 nm, Epot= -2.88894e+06 Fmax= 2.80767e+05, atom=
2883
Step=   14, Dmax= 1.1e-01 nm, Epot= -2.95328e+06 Fmax= 1.33061e+05, atom=
2883
Step=   15, Dmax= 1.3e-01 nm, Epot= -3.03044e+06 Fmax= 2.52114e+05, atom=
2881

step 16: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
tMPI error: Receive buffer size too small for transmission (in valid comm)
Abort (core dumped)

I don't understand what happend. Please can you help me? How i can reduce
timestep?

Em ter, 18 de set de 2018 às 08:36, Justin Lemkul <jalemkul at vt.edu>
escreveu:

>
>
> On 9/18/18 12:42 AM, Mario Andres Rodriguez Pineda wrote:
> > These were the errors until the moment of executing the minimization:
> >
> > After adding ions grompp:
> > NOTE 1 [file topol.top, line 37566]:
> >    System has non-zero total charge: -18.999999
> >    Total charge should normally be an integer. See
> >    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> >    for discussion on how close it should be to an integer.
> >
> > minimization mdrun
> > step 16: One or more water molecules can not be settled.
> > Check for bad contacts and/or reduce the timestep if appropriate.
> > Wrote pdb files with previous and current coordinates
> > tMPI error: Receive buffer size too small for transmission (in valid
> comm)
> > Abort (core dumped)
> >
> > In attach send you the mdp archive for minimization run.
>
> The mailing list does not allow attachments.
>
> Use the -v flag of mdrun to track the energy and forces at every step
> until the crash to see what's going on and where the maximum force is
> acting. There's probably a bad contact somewhere that can't be relaxed
> and you need to investigate why that's happening.
>
> -Justin
>
> > Thanks for your help
> >
> > Em seg, 17 de set de 2018 às 19:56, Justin Lemkul <jalemkul at vt.edu>
> > escreveu:
> >
> >>
> >> On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote:
> >>> Hi everyone.
> >>> I'm trying simulate a protein in water followin lysozyme tutorial using
> >>> gromacs 2016.3. When triying minimize the system after make the box and
> >>> insert a salt concentration the minimization has been stoped sendingme
> >> the
> >>> following error:
> >>>
> >>> step 16: One or more water molecules can not be settled.
> >>> Check for bad contacts and/or reduce the timestep if appropriate.
> >>> Wrote pdb files with previous and current coordinates
> >>> tMPI error: Receive buffer size too small for transmission (in valid
> >> comm)
> >>> Abort (core dumped)
> >> Water SETTLE problems are not unusual in energy minimization and are
> >> often resolved. If, however, such a message immediately precedes a
> >> failure, then you have a serious problem with either the coordinates or
> >> topology. mdrun prints out which atom is experiencing the maximum force,
> >> so start by looking there, as well as reviewing your notes about what
> >> warnings pdb2gmx or grompp may have issued (but surely you wouldn't have
> >> ignored any, right? :).
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Virginia Tech Department of Biochemistry
> >>
> >> 303 Engel Hall
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
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> >
> >
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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> Gromacs Users mailing list
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-- 
*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*
*UNAL- MEDELLÍN *