Banafsheh Mehrazma wrote:
Hi everyone;
I wonder what's the difference between fixing and freezing and
position restraining?
I know how to position restrain, but I don't have any idea how we can
fix or freeze.
So I would be glad if you tell me exactly, how we can fix the solute
while the solvent is not, and vice versa. :)
Freezing is done via freezegrps (and related settings) in the .mdp file. The
positions of the frozen atoms are invariant.
Restraining simply applies a biasing potential to the atoms such that
displacement is disfavored. The strength of the restraint is controlled by the
force constant in the posre.itp file.
-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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