[gmx-users] about g_hbond

[lina]

I got it.  I should have outputted the -hbn file.


Thanks,

On Thu, May 12, 2011 at 1:09 PM, lina <lina.lastname at gmail.com> wrote:
> /* y-label: "Hydrogen Bond Index" */
>
> is it relevant to the total number of hydrogen bonds?
>
> such as
> /* XPM */
> /* x-label: "Time (ps)" */
> /* y-label: "Hydrogen Bond Index" */
> /* type:    "Discrete" */
> static char *gromacs_xpm[] = {
>
> A-b : "51 84   2 1",
>
> b-C : "51 95   2 1",
>
> 84, 95?
>
> Thanks,
> On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> lina wrote:
>>>
>>> Hi,
>>>
>>> For group A, b, C.
>>>
>>> It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
>>>
>>> But I don't know how to get the number of residues of b forming both
>>> with A and B at the same time. namely b-A&C, not with AC group.
>>>
>>
>> There's no direct way to do it, but from the output files of g_hbond it can
>> be done.  You'd need the .xpm files of A-C and B-C hydrogen bonds, and write
>> some script that parses the .xpm files, and whenever there is an entry of
>> A-C in the same frame as B-C, then you have a hydrogen bond mediated between
>> the two.
>
>> There's lots of discussion in the list archive about water-mediated
>> hydrogen bonds that is likely applicable here.
>>
>> Note that if you're using g_hbond in version 4.5, there is an important bug
>> that was fixed just yesterday:
>>
>> http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html
>>
>> -Justin
>>
>>> Thanks,
>>> --
>>> Best Regards,
>>>
>>> lina
>>>
>>>
>>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
>
>
> --
> Best Regards,
>
> lina
>



-- 
Best Regards,

lina