[gmx-users] gromacs error in vacuum preparation simulation
jalemkul at vt.edu
Mon Mar 11 23:31:28 CET 2019
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
As the message says, you shouldn't be using PME for this system. In
vacuum, you should be using plain cutoff electrostatics with infinite
Justin A. Lemkul, Ph.D.
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