Thank you again for your reply<br><br><div class="gmail_quote">On Wed, Mar 16, 2011 at 7:35 PM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
2-When you limit your sampling phase space,it can make some Errors,<br>
Because you may ignore some important regions(where you don't know them and you can't predict there).<br>
</blockquote>
<br>
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.<br>
<br>
... snip ...<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Is it possible to do Umbrella Sampling while the drug be free to rotate<br>
along with oscilation in windows?<br>
</blockquote>
<br>
sure, but you will have more convergence problems.<br>
<br>
Chris.<br>
<br>
On Tue, Mar 15, 2011 at 9:49 AM, <chris.neale at <a href="http://utoronto.ca" target="_blank">utoronto.ca</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
1. yes. it is acceptable. It is different, but neither method is de facto<br>
better.<br>
<br>
2. to enhance convergence by limiting the amount of phase space that must<br>
be sampled. Changing the restraints can change the profile, but if you care<br>
only about the integrated standard binding free energy then it does not<br>
change the converged result. See, for example, D. L. Mobley, J. D. Chodera,<br>
K. A. Dill. "On the use of orientational restraints and symmetry number<br>
corrections in alchemical free energy calculations", ...<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
Dear All<br>
Afew question about Pulling in Umberella Sampling<br>
<br>
1-the goal of pulling is making some primary structures (in different<br>
distances) to do umberella sampling for each one of them.<br>
I can make these states by transporting my ligands along a vector to<br>
prepare these primary structures.Is this correct?Now I can do US for each<br>
one!without any need to doing pulling.<br>
<br>
2-Why do we keep fix the relative orientation of Protein-ligand during the<br>
pulling ? I think changing the orientation of ligand during the<br>
pulling(suppose the protein is restrain) can chang our result?<br>
Because our umbrella sampling maintain this orientation <a href="http://too.am" target="_blank">too.am</a> I right?<br>
<br>
Thanks in advance<br>
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</blockquote></div><br>