[gmx-users] Justin Tutorial - Protein-Ligand

[Justin A. Lemkul]

Steven Neumann wrote:
> Dear Gmx Users, Dear Justin,
>  
> As I read in your tutorial you restrained the ligand during the 
> quilibration: NVT and NPT. My questions is: is it required?
> Why cant we simply restrain the protein and let the ligand and water to 
> move around? Will there be a huge difference?
>  

Do what suits your system best.  If the ligand position requires refinement, let 
it move during equilibration.  Maybe you might want to do it in steps - protein 
and ligand restrained, then just protein restrained, etc.

-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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