[gmx-users] Indx file making

[Tsjerk Wassenaar]

Salaam Aleikum,

In addition it is worth to note that the standard groups gromacs uses
include Protein and Non-Protein, which you can use for temperature coupling
without using an "external" index group.

Tsjerk

On 12/27/05, Itamar Kass <ikass at cc.huji.ac.il> wrote:
>
>
>   Shalom,
>
> You can use make_ndx. Using this you can create a new group from the
> combination of other groups (e.g. "2 | 3" will combine groups 2 and
> 3).  thane you can rename it and put it in your mdp file.
>
> Cheers.
>
>
> On Dec 27, 2005, at 2:42 PM, hnam wrote:
>
> >
> >
> > In the name of God
> > I have three group in my system ,Protein ,Sol, Na+ ,how can i
> > create these
> > group at index file or how can i make proper index file for my system.
> >
> > Thank you very much in advance
> > Institute of  Biochemistry  and  Biophysics (IBB)
> > Tehran University
> > P.O.box 1417614411
> > Tehran
> > Iran
> >
> >
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>
>
> ===========================================
> | Itamar Kass
> | The Alexander Silberman
> | Institute of Life Sciences
> | Department of Biological Chemistry
> | The Hebrew University, Givat-Ram
> | Jerusalem, 91904, Israel
> | Tel: +972-(0)2-6585194
> | Fax: +972-(0)2-6584329
> | Email: ikass at cc.huji.ac.il
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> itamar_homepage.html
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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