[gmx-users] Pulling

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Mar 16 17:05:31 CET 2011

> 2-When you limit your sampling phase space,it can make some Errors,
> Because you may ignore some important regions(where you don't know  
> them and you can't predict there).

I agree with the idea that underlies your point, but it is not a  
problem. You don't need to sample all intervening phase space, just  
converge one well defined part of it. Read that paper again, and some  

... snip ...

> Is it possible to do Umbrella Sampling while the drug be free to rotate
> along with oscilation in windows?

sure, but you will have more convergence problems.


On Tue, Mar 15, 2011 at 9:49 AM, <chris.neale at utoronto.ca> wrote:

> 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", ...
> Chris.
> -- 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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