Hi Chris My windows are restrained obviously using the force constant in the mdp file. The trajectories that I have viewed are those of the individual biased sampling windows. I have not put on the unbiased simulations yet. There is also the following issue: The simulations involve two identical molecules containing hydrocarbon chains. I calculate the PMF to take a specific hydrocarbon chain of one molecule out of a specific site on the neighbouring molecule. When this guest chain goes out, other chains can go in (intramolecular or intermolecular). Will this affect the profile?
Gavin chris.ne...@utoronto.ca wrote: > Your windows are restrained. The PMF that you get out of WHAM is a > representation of the relative sampling after removing the umbrella > biases. Sounds like you are saying that you look at the still-biased > trajectories and you see different a different distribution of states > than you do in the de-biased PMF..... not sure what the problem is > here. Perhaps go back to some review literature on US. > > Now, if you saw more bound than unbound in unrestrained simulations, > then that's a different story, but that doesn't appear to be what you > are talking about. > > Chris. > > -- original message -- > > Hi all > > I have performed a PMF simulation of taking part of a molecule out of > the cavity of a host using umbrella sampling. The free energy curve > suggests that the guest prefers to be outside the host as the bound > state is higher in energy, or the free energy difference to go in is > positive. However when I view the trajectories for each window it > appears that there is always more bound states than unbound. This leads > me to doubt my free energy profile? > > 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
