[gmx-users] trivial question about water molecules

[Justin Lemkul]

Please keep the discussion on the gmx-users mailing list.

On 1/22/16 3:42 AM, Marta Wisniewska wrote:
> Hello Justin,
>
> thank you for your response. I know about that way. I'd like to calculate it on
> piece of paper. I'va already tried do this. But I have small problem and the
> solutions is not in agreement with data from topolgy file. How can I calculate this?
>

I don't understand what the question is.  How many ions were added?  What data 
do you think are in disagreement?  genion really does a very simple operation, 
so it should be quite obvious what happened.  The calculation is nothing more 
than simple arithmetic.

-Justin

> Thank you in advance,
> Marta
>
> Date: Thu, 21 Jan 2016 12:30:36 -0500
> From: Justin Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Subject: Re: [gmx-users] trivial question about water molecules
> Message-ID: <56A115BC.9020404 at vt.edu <mailto:56A115BC.9020404 at vt.edu>>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 1/21/16 11:47 AM, Marta Wisniewska wrote:
>  > Hello Gromacs Users;
>  >
>  > I'd like to calculate the # of replaced water molecules by sodium chloride
>  > in my system . I added a 0.15M concentration of NaCl. How can I calculate
>  > the number of water molecules, which are replaced by ions?
>  >
>
> genion replaces a water molecule with an ion, so the number of waters replaced
> equals the number of ions added.
>
> -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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