The tricky part is that if you look at the first line in the file
hbm.xpm you are looking at the bottom row of the matrix when displayed
with gimp or after converting to xpm2ps. The same line corresponds to
the first hbond in hbn.ndx. That sentence in the manual is therefore a
bit ambiguous.
Erik
Carla Jamous skrev 2010-10-15 13.29:
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
<mailto: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 <mailto:er...@xray.bmc.uu.se>
http://folding.bmc.uu.se/
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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/
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