[gmx-users] Re: g_hbond in version 3.4.1 vs rest (Especially higher one)

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 30 21:11:11 CEST 2008

Anil Kumar wrote:
> Dear Justin,
> Sorry for sending personal email regarding the query related to gromacs.
> Actually long back i had send this query many times on forum but didn't
> got any reply.

Nevertheless, I don't solicit extra work.  Please keep all Gromacs-related 
questions on the mailing list.

The risk you take is that the person from whom you're asking advice has no idea 
what the problem is.  That is the case here.  I have never had a need to use 
g_hbond -hx, so I have no idea what the problem is.

It sounds like there *may* be some problem with this option in newer versions of 
Gromacs, but that is pure speculation.  If you can show output from each version 
to compare, that would be useful, clearly indicating the version of Gromacs used 
to obtain each, along with the *exact* command line used to produce the output, 
maybe that will be illustrative to someone who knows more than I.  Be sure to 
also describe how each version of Gromacs was compiled.  As described repeatedly 
on the gmx-users list, using gcc-4.1.x often causes analysis tools (among 
others) to produce strange results.


> When i use g_hbond with -hx option to know the pattern of hydrogen bond
> then i got very surprising result in higher version (3.2.1/3.3.1 etc0 with
> output under n-n column (which is illogical!).
> Earlier i was using 3.4.1 and here i never come across this kind of
> strange hydrogen bond.
> Would you kindly let me know where is the problem!
> Even i had tried g_hbond with same PDB on 3.4.1 and higher...in case of
> 3.4.1 it gives correct hydrogen bond pattern...but in higher version it
> shows hydrogen bonds under n-n column.
> Your expert comments will be highly appreciated.
> Waiting for kind response.
> Thanks,
> With Warm Regards
> -
> ANIL KUMAR(Senior Research Scholar)             |
> Graduate Student of Prof. S. Durani's Research   Group |
> Bio-Organic Lab No-336(2nd Floor),               |
> Dept. of Chemistry,
> Indian Institute of Technology Bombay,
> Powai, Mumbai-400076,
> Ph. No.+91-22-25764780 (Lab)
>        +91-22-25764168 (Lab)
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> "Education is a progressive discovery of our ignorance"
> - Will Durant
> ----------------------------


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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