Hi Thomas A few points below under your points
Thomas Schlesier wrote: > Yes you are right, should be between 0 and >0. > > Do you have a window for a distance equal 0? Yes > > > This window should behave similar to the RDF-analysis. Because there > are "no directions". It doesn't. By this I mean the zero point of the reaction coordinate does not give a free energy minimum (actually the minimum is shifted to the right) whereas from the reversible work theorem it does. > > Or to reformulate the problem. > We make an umbrella window for a distance of 1. If particle stays > there everything is fine. If particle moves to 0, it should be also > fine (particle sees a force of k*1). If paticle moves to -1, it should > see a force of k*2, but instead, the distance is 0 -> no force. I don't understand from "if particle moves ......" > If you have the umbrella window centered at 0 this problem vansihes -> > if particle move it sees always a force. > > But one thing gives me headaches. I don't have this problem in my > pulling simulation, because the distance between my reference and > pulled group can not become zero: > But concerning the reaction coordinate it will have a similar flaw > like the RDF i think: It doesn't matter in wish direction the particle > moves (left or right) due to the distance we would always say it moves > along the reaction coordinate. In reality it moves sometimes in the > negative direction of the reaction coordinate, but we always say it's > a positve distance -> so positive value on the reaction coordinate. > For an isotropic system this would not matter, but for system which we > have a anisotrop reaction coordinate it should matter. My system is isotropic > > > Greetings > Thomas > > > > Am 17.02.2012 17:07, schrieb [email protected]: >> Hi Thomas Many thanks for the reply again. At larger distances the two >> curves match up quite well. The curve from the reversible work theorem >> is better behaved and smoother but this could be solely due to >> statistics. I am slightly confused about your statement "If the small >> circle moves between 0 and any value <0 everything should be fine." Do >> you not mean 0 and any value >0 ? Cheers Gavin Thomas Schlesier wrote: >>> > 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 [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 the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
