Justin A. Lemkul skrev 2010-09-10 22.33:
ceste...@unsl.edu.ar wrote:
Hi all:
I´m using gromacs version 4.0.2 and a box type truncated octahedron for
the MD simulation.
I need to analyze hydrogen bonds with solvent (water)insertion.
I used the following command:
g_hbond –f *.xtc –s *.tpr –n *.ndx –num num.xvg –dist *.xvg –ang
*.xvg –a
45 –r 0.3 –ins.
I selected acceptor and donor grups and solvent grup.
The problem is that the file num.xvg is the same with direct hydrogen
bonds (without solvent) and the output insert.dat is empty.
Why is this?
I don't think the -ins option has been functional for some time, and
(I presume) it is for this reason that it was removed prior to the 4.5
release.
-Justin
Indeed. I am probably the one person who has spent most time developing
g_hbond over the last two years or so and I'm not exactly sure of how
the -ins option is supposed to work, why it doesn't work, and how it
interferes with other g_hbond functionality. Don't expect it to be fixed
soon, at least not by me. More likely, it will turn up as a separate
tool when the analysis tools become more modular some time in the future.
Erik
Any help would be appreciated
Carmen
--
-----------------------------------------------
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/
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