Thank you again for your reply On Wed, Mar 16, 2011 at 7:35 PM, <[email protected]> wrote:
> 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 >> -------------- next part -------------- >> > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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