> > Michael McGovern wrote: > > Hi everyone. I'm having some trouble using g_wham to analyze some > > results. I have some simulations from gromacs 3.3 using the pull > > code. I'm using the latest version of g_wham to analyze the results, > > which the help file says is ok, using the -ip option. > > > > I've gotten almost everything to work, and it generates histograms > > that seem perfectly reasonable, but sometimes the free energy it > > outputs is completely flat, with each bin having a free energy value > > of 0. > > > > I've played around with the -b and -e options using only part of my > > data, and sometimes it gives non-flat free energies, other times not. > > I see no logic to when it works and when it doesn't. My data does > > have good overlap of the histograms, and it sometimes converges even > > when I use data that have no overlaps, so that doesn't seem to be the > > problem. > > > > I'm completely confused. Does anyone know what could cause this? > > > > > > Hi Micheal, > > how large is your data? Could you send me a tar.gz of your pdo files? I > would like to make sure that there is no bug in g_wham. > > Jochen > > I had this problem also when I tried to calculate dimerization free energies using umbrella sampling and g_wham. The problem seemed to occur every time I included .tpr files that contained configurations in which there were no more interaction between the previously dimerized set. What I mean is, when I monitored the LJ and Coul interactions between my molecules, I found out that there would be no more interaction beyond, lets say, 2.1 nm (distance between COM of my molecules). When I included the 2.0, 2.1, 2.2 nm etc windows in my g_wham analysis, I got a flat free energy graphic. Just wanted to add that to the post. Thanks
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