Yes, my profile seems normal, the only problem are the units in the x-axis, because I expected them to be in the range of the dimensions of the channel. I will try if I see differences with the other options you proposed, anyway. Thanks a lot for your help!! Best wishes, Rebeca.
> Date: Thu, 31 May 2012 15:52:48 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Re: boundaries in PMF > > > > On 5/31/12 3:51 PM, Rebeca García Fandiño wrote: > > OK, > > however, just one point about your last comment: > > > > > I suspect this is why g_wham is finding a range of values only equal to > > half of > > > your expected reaction coordinate; it is considering only the positive > > > displacement along the reaction coordinate. > > > > It seems like all the channel is explored, not only one half. If g_wham was > > only > > considering the positive displacement I should see a profile for just one > > half > > of the channel, shouldn´t I? and I can see a profile typical for the entire > > channel. > > > > Then perhaps it's just a small g_wham output bug (boundary values). You > didn't > mention that your profile looked normal ;) > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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
-- 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
