[gmx-users] Pulling ligand out of protein for umbrella sampling

[Suhaib Shekfeh]

Dear GMX-users

In an old post in this list about umbrella sampling in gromacs and the pull
code, (
http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/w3NmJ69y/md-pull-code-in-umbrella-sampling
)
Christopher Neale gave an interesting comment about the case of pulling a
ligand out of a protein, especially when some of first contacts between the
two pull groups can cause improper sampling as they need other orthogonal
X/Y degrees of freedom

his suggested solution was as follows: "Personally, I would solve this by
adding a second pull group with a flat-bottom potential that acts only on X
and Y to keep the drug within a cylinder that extends along Z away from
your protein. However, you would need to modify gromacs source code for
this (I have some posts on the uses lists over the years about how to do
this). An alternative solution is to define an order parameter that acts in
all 3 dimensions, although you may need to compute the free energy of releasing
this restraint (a) in the binding pocket and (b) at large separations where
your PMF flattens out to zero."

I would like to ask Christopher or other expert users here to explain more
about these solutions, especially which one of them is easier?


-- 
Suhaib Shekfeh
Department of Pharmaceutical Chemistry
Gazi University Eczailik Fakültesi (Faculty of Pharmacy)

LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255