[gmx-users] Re: Relaxed frozen groups

[Justin A. Lemkul]

Zack Scholl wrote:
>>> Zack Scholl wrote:
>>> Hi all-
>>>
>>> Is it possible to freeze a group of atoms only partially in a
>>> direction?  For instance, could I freeze a group inside a box of a
>>> definite size?
>>>
>>>
> 
>> Not by defining a box, as such, but you can freeze any subset of atoms with a
>> suitable index file that defines the desired freezegrps.
>>
>> -Justin
> 
> I'm sorry, I didn't phrase my question clearly.
> Can I set a group so that it can move - but only within a specified region?
> Or, even better, possibly attach some group to a strong spring that
> does not allow it to move very far, but does not completely restrict
> the motion of the group?  I don't want to use freezegrps because it
> would completely restrain the position of an atom- but I would like to
> restrain the movements of the atom to within a defined region (e.g. a
> small box).

The pull code might be applicable here, applying a harmonic restraint to a group 
to keep it close to some reference location.  You can set relative or absolute 
reference positions; see the manual.

-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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