[gmx-users] Verlet scheme

[Justin Lemkul]

On 2/14/17 8:24 AM, chemocev marker wrote:
> Hi
> I am using gromacs-5.1.1 version and getting this note and also the pfb2gmx
> gives me the value of the net charge but this information is not written in
> the topology file.
>
> How to correct this note.
>
> ions.mdp did not specify a value for the .mdp option "cutoff-scheme".
>   Probably it was first intended for use with GROMACS before 4.6. In 4.6,
>   the Verlet scheme was introduced, but the group scheme was still the
>   default. The default is now the Verlet scheme, so you will observe
>   different behaviour.
>

Use correct settings in the .mdp file :)  You're probably still hanging on to 
old .mdp files that don't have updated keywords.

http://manual.gromacs.org/documentation/5.1.4/user-guide/mdp-options.html

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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