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
others.
... 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.
Chris.
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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