[gmx-users] g_hbond solvent insertion problem

Erik Marklund erikm at xray.bmc.uu.se
Sat Sep 11 10:14:38 CEST 2010

  Justin A. Lemkul skrev 2010-09-10 22.33:
> cesteban at 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.

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

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