I'm sorry I don't understand, because your last answer doesn't correspond to what's written in the manual. I'm using gromacs 4.0.3 and the manual says:
-hbm: existence matrix. Ordering is identical to that in -hbn index file. And yes, my trajectory is concatenated the way I intended to, but I will check anyway. Carla On Fri, Oct 15, 2010 at 1:23 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > Carla Jamous skrev 2010-10-15 12.05: > >> Hi everyone, >> >> >> please I need some help on g_hbond. >> >> I concatenated 3 trajectories. I ran g_hbond on the concatenated >> trajectory. I got the result of h_bonds. >> Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get a >> different result, it means: if I take the first 10ps of my concatenated >> trajectory and I run g_hbond on these 10ps. I get some H-bonds eg. >> Gly(N)...H(gly)...O >> but this same H-bond doesn't appear >> in the first 10ps of my concatenated trajectory's HBmap. >> >> Please does anyone have an idea where I might have done a mistake? >> >> Thank you, >> Carla >> >> Have you confirmed that the concaternation was done the way you intended? > > > -- > ----------------------------------------------- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se http://folding.bmc.uu.se/ > > -- > 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 >
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