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
--
========================================
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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