lq z wrote:
Dear GMXers,
I can apply harmonic bond, angle, and dihedral restraints between two
molecules (3 atoms on one, and one atom on the other one). If yes, how
to set it up in the topology file?
They have to be in the same [moleculetype].
Question 2: Can I apply distance restraint between mass center of some
atoms in one molecule and ONE ATOM in the other molecule?
Yes, with the pull code and suitable index groups.
Question 3: Can those restraints be lambda (in alchemical free energy
simulation) dependent?
Yes, see the manual.
-Justin
You may have known what I'm trying to do: Change one molecule to dummy,
so I need restrain it at dummy state while no restraint is wanted at
real state.
Thanks,
Luke
--
========================================
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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