Justin In regard to my query regarding the cut-offs at zero with no pbc. I assume its is fine to have box dimensions (0 0 0) to comply with the definition of a vacuum simulation. I am just worried that there may be some default cut-off that I am not aware of.
Cheers P.S I have plotted the pullx.xvg files for the distances between the COMs of the molecules in the problematic windows. As was the case with plotting with g_dist there is significant population of the at the extremities of the window compared to that around the average r0. Justin A. Lemkul wrote: > > > chris.ne...@utoronto.ca wrote: >> I have seen this before, and there are a few possible reasons, but >> I'm still waiting to see that histogram with two peaks >> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html). >> It's really hard to help you when we have to guess what the problem >> looks like... or perhaps you posted it and I missed it? > > The histogram was posted several days ago: > > http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html > > The attachment link is: > > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin > > > -Justin > >> >> -- original message -- >> >> O.K thanks anyway >> >> >> Justin A. Lemkul >> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html >> >>> >>> >>> Gavin Melaugh wrote: >>>> Thanks Justin >>>> >>>> Have you any idea why when generating umbrella histograms for the >>>> pmf I >>>> would get two peaks in the histograms above a distance of 2 nm, but >>>> below 2 nm I get well behaved histograms that lead to a very >>>> good profile in the pmf. To the best of my knowledge the >>>> configurations >>>> are all very well equilibrated at their respective COM distances. >>>> Umbrella sampling is performed on all windows using a force >>>> constant of >>>> 1000 kj/mol at 600 K. >>>> >>> >>> Sorry, no clue. >>> >> >> > -- 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/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/mailing_lists/users.php
