[gmx-users] g_hbond solvent insertion problem

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 10 22:33:29 CEST 2010

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.


> Any help would be appreciated
> Carmen


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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