[gmx-users] genion -conc give the wrong number of multi-valent counter ion

[Justin Lemkul]

On 6/16/17 7:14 AM, Quyen V. Vu wrote:
> Dear GMX developer,
> I don't know this mailing list is suitable for posting issue or not, if
> not- forgive me.
> 
> I want to report about gmx genion module
> 
> If i want to add concentration of salt by -conc option, it just correct for
> monovalent salt (eg. NACL).
> 
> For multivalent salt(MGCL2), if I use -pname MG -nname CL -conc X -neutral
> , it wil treat MG as monovanlent cation and give the wrong number of ions
> add into my system, so  I have to use -np and -nn option to get correct the
> number of ions.
> 

If you set the correct value of -pq then you'll get the right result.  genion 
defaults to assuming everything is monovalent and if that's not the case, you 
have to provide correct instructions via the command line.

-Justin

-- 
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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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