[gmx-users] (no subject)

Justin Lemkul jalemkul at vt.edu
Sun Sep 23 18:31:36 CEST 2018

On 9/23/18 12:11 PM, AKANXA TIWARI wrote:
> Hi
> During simulation of protein after giving grompp ions command i got a note
> what should i do.
>   NOTE 3 [file ions2.mdp]:
>    You are using a plain Coulomb cut-off, which might produce artifacts.
>    You might want to consider using PME electrostatics.

This note is harmless if the .tpr file is only being used to add ions. 
Trying to use PME (e.g. by copying an .mdp file that is used for EM or 
MD) will trigger a fatal error due to the non-zero charge of the system. 
So .mdp files specifying plain cutoffs are necessary for adding ions, 
but should not be used for anything else.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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


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