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