[gmx-users] gromacs error in vacuum preparation simulation

Justin Lemkul 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
> 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
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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