Hi Chris I have generated a histogram from the my.data file and i get a histogram with the exact same profile as that generated from g_wham. Also on comparison of the dx, dy, dz values in the g_dist file with the vaules in the pullx.xvg file I notice that the magnitudes of the vectors are identical but their signs are opposite. e.g. g_dist file -2.2756047 -0.0369981 0.3126130
pullx.xvg file 2.2756 0.036998 -0.312613 Cheers Gavin Please note that there is a significantly more interaction between the molecules below 2 nm whereas above they interact very weakly (from viewing the trajectories) chris.ne...@utoronto.ca wrote: > Yup, just got the link. Thank you for posting, and sorry that I missed > it. It seems possible that Justin is correct and you'll get good data > if you take it out of the pullx.xvg file (perhaps the g_dist tool is > wrapping pbc for you). > > 1. How big is your box definition in your .gro file? > > You are right that you need the actual distance, which is not provided > directly. I think you want this (assuming that cols 5,6,7 give you the > dx,dy,dz, which I believe that they do): > > cat pullx.xvg | grep -v '[#|@]' | awk '{print > $1,sqrt($5*$5+$6*$6+$7*$7)}' > my.data > > 2. If you do this to a window > 2.0 nm and generate a histogram, do > you still get two peaks? > > A quick look at the src/tools/gmx_dist.c file indicates that it should > only apply periodicity if you give it a .tpr where PBC was applied -- > you can check this by comparing the dx, dy, dz out of g_dist with the > values in pullx.xvg > > If the problem is not solved here, then you can send me off-list all > the files needed to run a window around 2.5 nm plus all the output > that you have obtained from a single run and I'll take a look if you > wish. If you'd rather not do that and there are still problems, then > perhaps you can post a step by step from the beginning where you copy > and paste absolutely all of your commands (e.g. paste the *exact* > grompp, mdrun, g_dist, etc. commands) and the complete .mdp file and > the last line in your starting .gro file. > > Chris. > > -- original message -- > > [gmx-users] pbc atom > Gavin Melaugh gmelaugh01 at qub.ac.uk > Tue Aug 24 17:19:45 CEST 2010 > > * Previous message: [gmx-users] pbc atom > * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > > Hi Chris > > Yeah I posted the histograms a few days ago as Justin said. Did you get > the link? > > Gavin > chris.neale at 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? >> >> -- 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. >>>> > > -- 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