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

[Michael Tallhamer]

On 6/25/03 3:58 AM, "David van der Spoel" <spoel at xray.bmc.uu.se> wrote:

> 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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I have a PyMOL extension program that will allow you to select whatever
potions of the system you wish to freeze visually using PyMOL and it will
then write the index file for you from your selection. I can send pictures
and a index file as an example of what I am talking about if you wish. I
routinely use it for systems with 68,000 atoms plus when typing by hand
would be a ridiculous task.

Michael Tallhamer
Graduate Research Asst
Cleveland State University
Cleveland Ohio 44115
216-875-9723
m.tallhamer at csuohio.edu