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 <schl...@uni-mainz.de
<mailto:schl...@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 <golesan...@gmail.com
<mailto:golesan...@gmail.com>>
Subject: Re: [gmx-users] water medium
To: jalem...@vt.edu <mailto:jalem...@vt.edu>, Discussion list for
GROMACS users
<gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
Message-ID:
<aanlktikvksqelk-hu04toj6a_fg2iqwrlcx0xj_jn...@mail.gmail.com
<mailto:aanlktikvksqelk-hu04toj6a_fg2iqwrlcx0xj_jn...@mail.gmail.com>>
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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 <jalem...@vt.edu
<mailto:jalem...@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
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