[gmx-users] gromacs error in vacuum preparation simulation
Mario Andres Rodriguez Pineda
mandres at iq.usp.br
Tue Mar 12 19:45:37 CET 2019
Thanks, for your help.
Em seg, 11 de mar de 2019 às 19:31, Justin Lemkul <jalemkul at vt.edu>
> 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
> > 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 A. Lemkul, Ph.D.
> Assistant Professor
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*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*
*UNAL- MEDELLÍN/ IQ- USP*
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