[gmx-users] gromacs error in vacuum preparation simulation

[Mario Andres Rodriguez Pineda]

Thanks, for your help.

Em seg, 11 de mar de 2019 às 19:31, Justin Lemkul <jalemkul at vt.edu>
escreveu:

>
>
> On 3/11/19 5:45 PM, Mario Andres Rodriguez Pineda wrote:
> > If i don't use -maxwarn option they send me the same error.
>
> Omitting -maxwarn won't fix problems, but it is a very bad habit to
> casually use -maxwarn as it overrides critical problems with your input.
>
> > 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
>
> As the message says, you shouldn't be using PME for this system. In
> vacuum, you should be using plain cutoff electrostatics with infinite
> cutoffs (rlist=rcoulomb=rvdw=0).
>
> -Justin
>
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-- 
*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*

*UNAL- MEDELLÍN/ IQ- USP*

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