[gmx-users] Justin Tutorial - Protein-Ligand

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 1 15:13:58 CET 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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