Hello, I was following your argument but then doesnt pull_dim=Y Y Y mean it pulls in all directions at once? I use pull_dim=N N Y , or just 1 pull direction and it works. I might be wrong, but would be interesting if you got it to work like that for a small molecule.
Stephan Watkins -------- Original-Nachricht -------- > Datum: Fri, 17 Feb 2012 16:34:22 +0100 > Von: Thomas Schlesier <schl...@uni-mainz.de> > An: gmx-users@gromacs.org > Betreff: [gmx-users] pull-code > Hi Gavin, > if i remember correctly it was a system about pulling a ligand from a > binding pocket? > To make the system simpler we have a big circle and in the middle a > small circle. And we assume that the potential minimum for the > interaction between both circles is when the small cirlce is in the > middle of the large circle. > Now we do the Umbrella sampling. For a window which is centered at a > distance which is sligthly greater then 0, we will get problems. Assume > small circle is sligthly shifted to the right. And the other windows are > also in this dircetion. (-> reaction coordinate goes from zero to the > right dircetion) > If the small circle moves between 0 and any value <0 everythig should be > fine. But if the small circle moves to the left, we will also get a > positive distance. Problem is from the above defined reaction coordinate > it should be a negative distance. So we are counting the positive > distances too much. > To check this, you could use *g_dist* to calculate the distance for both > molecules for the problematic windows. Then project the resulting vector > onto your reaction coordinate. Then you should see the crossings between > the right and left side. > > How do the two free energy curves compare for larger distances, where > you can be sure, that you do not have this 'crossing problem'? > > Greetings > Thomas > > > > --------------------------------------------------------------------------------- > > > Hi all > > I am returning to a query I had a few weeks ago regarding a discrepancy > between two free energy curves. One calculated using umbrella sampling, > the other calculated via the reversible work theorem from the RDF. There > is sufficient sampling of the dynamics in the RDF so this method is > viable. > Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y. > The free energy curve from the pull-code method does not give me a > minimum at the zero value of the order parameter whereas the RDF method > does. Someone said before about double counting of positive distances at > small values of the order parameter and therefore information is lost at > very small distances. > > Is this correct? > I am slightly concerned that my curves are not giving me the correct > information involving a very important state in my reaction coordinate. > > Also when this dist restraint (which cannot be negative) is implemented > are there issues with the normalisation of the histograms from g_wham? > > Cheers > > Gavin > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://www.gmx.net/de/go/freephone/ -- gmx-users mailing list gmx-users@gromacs.org 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists