[gmx-users] Production run before starting Pulling

[faride badalkhani]

Dear Gromacs users,

I want to perform center of mass pulling simulations on a
nanostructure-drug structure. I performed MD simulations on the
nanostructure for 30 ns and it equilibrated well. then I docked the drun
into the nanostructure using Auto Dock Vina software. Now I want to know if
I should perform minimization, equilibration and production run on the
nanostructure-drug complex again. When I run MD simulations on the
nanostructure-drug complex obtained from docking, drug position changes
significantly.
Actually, what is the best approach for finding the starting configuration
for pulling?

Regards,
Farideh