[gmx-users] Pulling

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Mar 15 17:49:51 CET 2011

1. yes. it is acceptable. It is different, but neither method is de  
facto better.

2. to enhance convergence by limiting the amount of phase space that  
must be sampled. Changing the restraints can change the profile, but  
if you care only about the integrated standard binding free energy  
then it does not change the converged result. See, for example, D. L.  
Mobley, J. D. Chodera, K. A. Dill. "On the use of orientational  
restraints and symmetry number corrections in alchemical free energy  
calculations", ...


-- original message --

Dear All
Afew question about Pulling in Umberella Sampling

1-the goal of pulling is making some primary structures (in different
distances) to do umberella sampling for each one of them.
  I can make these states by transporting my ligands along a vector to
prepare these primary structures.Is this correct?Now I can do US for each
one!without any need to doing pulling.

2-Why do we keep fix the relative orientation of Protein-ligand during the
pulling ? I think changing the orientation of ligand during the
pulling(suppose the protein is restrain) can chang our result?
   Because our umbrella sampling maintain this orientation too.am I right?

Thanks in advance
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