[gmx-users] How to freeze the atoms at some specific area

[David van der Spoel]

On Wed, 2003-06-25 at 09:24, Jia-Lin Lo wrote:
> Let me make myself clear. I have a gro file
> ( for example, spc216.gro). If I want to freeze one side of 
> this cubic system. How should I write down the atom 
> numbers for this freeze group.   It's easy to write down 
> the atom numbers manually in this case. I just watch the 
> whole structure and mark the atoms at the same side.
> What should I do if this system is too large to be marked 
> by eyes.
Well, you have to have some kind of criterium, e.g. Z > 3 nm. If you
have that you can program it in a small script, that e.g. reads a pdb
file and generates an index file.
> 
> Jia-lin
> 
> 
> > I'm not sure, what you exactly want to do.
> > Please give more details.
> > 
> > Jia-Lin Lo wrote:
> > > Dear gmx users;
> > >      If I need to freeze the atoms at some
> > > specific areas. How should I write down the
> > > atom number for this group. I have tried  make_ndx and I think it can 
> > > just recognize
> > > the names of the atoms and residues. But it
> > > cannot tell me the atom number at some areas.
> > >     Any help or suggestions will be appriciated.
> > > Thanks in advance.
> > >  
> > > Jia-lin
> > > ==============================================================
> > > Jia-lin LO
> > > Dept. of Physics ,National Central University,
> > > Chung Li , Taiwan,
> > > e-mail : jllo at phy.ncu.edu.tw <mailto:jllo at phy.ncu.edu.tw>  Home page: 
> > > http://pooh.phy.ncu.edu.tw/~jllo/
> > > ==============================================================
> > 
> > -- 
> > Christoph Freudenberger
> > Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
> > 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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