[gmx-users] restraints between two molecules

[Justin A. Lemkul]

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
> 

-- 
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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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