[gmx-users] Re: water medium

[Justin A. Lemkul]

tahereh tekieh wrote:
> but it over writes on the previous status.
> 

Not if you use the right input.  Insert your first ion type with genion, update 
the topology, generate a new .tpr file and insert your second ion type, etc.  If 
you use the same .tpr file (containing only solvent) for each addition, you 
essentially re-set the system of interest back to solvent-only.  If you make 
changes to the system, those have to be accounted for.

-Justin

> On Wed, May 19, 2010 at 2:12 PM, Thomas Schlesier <schlesi at uni-mainz.de 
> <mailto:schlesi at uni-mainz.de>> wrote:
> 
>     Use genion multiple times.
>     If you want to insert Na+ and K+, then first use genion with one and
>     then with the other ion.
> 
>     Greetings
>     Thomas
> 
> 
> 
>     Message: 5
>     Date: Wed, 19 May 2010 11:37:09 +0430
> 
>     From: tahereh tekieh <golesang80 at gmail.com
>     <mailto:golesang80 at gmail.com>>
>     Subject: Re: [gmx-users] water medium
>     To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>, Discussion list for
>     GROMACS users
>            <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>     Message-ID:
>            <AANLkTikvKsQeLk-hU04toj6A_Fg2iqwRlCx0Xj_jntvL at mail.gmail.com
>     <mailto:AANLkTikvKsQeLk-hU04toj6A_Fg2iqwRlCx0Xj_jntvL at mail.gmail.com>>
>     Content-Type: text/plain; charset="iso-8859-1"
> 
> 
>     but genion only accepts one type of ion, how can we insert different
>     types?
> 
>     On Tue, May 18, 2010 at 3:38 PM, Justin A. Lemkul <jalemkul at vt.edu
>     <mailto:jalemkul at vt.edu>> wrote:
> 
>      > >
>      > >
>      > > tahereh tekieh wrote:
>      > >
>      >> >> dear friends
>      >> >> i want to simulate a water medium in which 5 types of
>     different ions flow
>      >> >> in it. how can i do that with gromacs?
>      >> >> thanks
>      >> >>
>      >> >>
>      > > Assuming they are monoatomic, you can use genion after you have
>     added
>      > > water.  If they are polyatomic, use genbox -ci -nmol (before
>     filling the box
>      > > with water).
>      > >
>      > > -Justin
>      > >
>      > > --
>      > > ========================================
>      > >
>      > > Justin A. Lemkul
>      > > Ph.D. Candidate
>      > > ICTAS Doctoral Scholar
>      > > MILES-IGERT Trainee
>      > > Department of Biochemistry
>      > > Virginia Tech
>      > > Blacksburg, VA
>      > > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>      > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>      > >
>      > > ========================================
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================