[gmx-users] Re: Re: couple-moltype of FEP (Justin A. Lemkul)

[Chunxia Gao]

Dear Justin:

What I mean is can I calculate the free energy of restraining the ligand in the binding site, since I put on distance restraint to the ligand and the protein?

Regards
Chunxia

Chunxia Gao wrote:
> Dear Justin,
>
> If I apply the pull code to the distance restraints, can I calculate the free energy of those restraints through g_bar? In what way?
>

The pull code and free energy code are independent.  I see no reason why you
could not proceed in the same manner as the free energy tutorial describes, but
with the addition of your restraint.

> and the pull code can only be applied to distance restraints, right? not angle or dihedral restraints?
>

Correct.

-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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