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

[Justin A. Lemkul]

Chunxia Gao wrote:
> 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?
> 

Ah, now I see.  I'm not sure, but I know the answer is out in the literature 
somewhere; various types of restraints are implemented in free energy 
calculations fairly routinely.

-Justin

> 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
> 
> --
> ========================================
> 
> 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
> 
> ========================================
> 
> 

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

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

========================================