[gmx-users] Do I need position restraint for umbrella sampling?

[Yoo Chan Myung]

Dear gmx users,

I'm trying to simulate membrane penetration with peptide(octamer) using
GROMACS-5.1.2. and I referred the Umbrella Sampling tutorial by Dr. Justin
Lemkul.

After 100 ps umbrella_NPT run, peptides confirmations are still kept in
their initial coordinates. However, after 10ns of umbrella_MD, I cannot get
reliable results for WHAM analysis because the confirmations are quite
deviated from the umbrella_NPT structures.
(plz, refer two results,
https://www.dropbox.com/s/maqwjww8nozmcn6/q_a.jpg?dl=0)

So, my question is should I have to use position restraint for moving
ligands? or just extend simulation time for umbrella_NPT to get equilibrium
structures for umbrella_MD?

Regards
Yoochan