[gmx-users] gromacs error in vacuum preparation simulation

[Mario Andres Rodriguez Pineda]

If i don't use -maxwarn option they send me the same error.
I see also this:
WARNING 1 [file topol.top, line 23986]:
  You are using Ewald electrostatics in a system with net charge. This can
  lead to severe artifacts, such as ions moving into regions with low
  dielectric, due to the uniform background charge. We suggest to
  neutralize your system with counter ions, possibly in combination with a
  physiological salt concentration.
Cheking the archive toppol.top this line is empty

I'm try to minimize the energy of my protein in vacum, whithout ions or
solvent

Em seg, 11 de mar de 2019 às 17:12, Justin Lemkul <jalemkul at vt.edu>
escreveu:

>
>
> On 3/11/19 3:20 PM, Mario Andres Rodriguez Pineda wrote:
> > Hi everybody
> > I want to do one dynamic simulation of one protein
> > i'm try to minimize the protein in vacum before the simulation runing but
> > gromacs send me this error:
> > -------------------------------------------------------
> > Program:     gmx grompp, version 2018.6
> > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991)
> >
> > Fatal error:
> > There was 1 error in input file(s)
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
> --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> --------------------------------------------------------------------------
> > this is the command that i use for minimization in vacum.
> > gmx_mpi grompp -f vacuum.mdp -c cbd212_box.gro -p topol.top -o
> > cbd212_vac.tpr -maxwarn 1
>
> Run grompp interactively if you want to see the actual error. It may
> also be printed to a log file from your queuing system. Also, never use
> -maxwarn.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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> Blacksburg, VA 24061
>
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>
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>
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-- 
*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*

*UNAL- MEDELLÍN/ IQ- USP*

*Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas *
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