If you position restraint the receptor or only use several residues at the 
binding site, in both cases you limit your sampling to a small part of the 
phase space and the PMF may not be accurate, since the receptor may undergo 
conformational change upon ligand binding.
Cheers
--Jianguo



----- Original Message -----
From: 范聪 <fanc...@nenu.edu.cn>
To: gmx-users@gromacs.org
Cc: 
Sent: Tuesday, 30 October 2012, 20:04
Subject: [gmx-users] steered pulling code on ligand-receptor complex


Hello, everyone!
    I'm a new user in gromacs, and now I have to perform a steered pulling code 
on a ligand-receptor complex. The ligand is to be pulled away from the binding 
site of the receptor, and umbrella sampling will be used to gain the PMF 
(potential mean force) curve. Then  binding energy of the ligand-receptor 
complex would be estimated.  The receptor contains 303 residues. While the 
ligand is pulling away, the whole receptor is restrained by posres, 1000 in x, 
y and z axis.
   Since the receptor is so large and umbrella sampling needs so much 
calculations, a very long time will be taken to complete the work.
   Now I have my question, is there anyway to reduce the taken time? Such as 
keeping only residues near the binding site to respect the whole receptor?
   Thank you all in advance!

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