[gmx-users] g_hbond on concatenated trajectory

Erik Marklund erikm at xray.bmc.uu.se
Fri Oct 15 13:23:30 CEST 2010

  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
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

More information about the gromacs.org_gmx-users mailing list