[gmx-users] g_hbond Issues

[Justin A. Lemkul]

Anil Kumar wrote:
> Dear Mark,
> 
> Thanks for your suggestions of including/using index file. This is fine 
> but is it not a cumbersome process to define for different length of 
> systems in this way! Since, one has to define/make the group for each 
> carbonyl group with other pairs!
> 

Using index files is one method, but Mark's additional comment of reading the 
help information is also quite poignant, especially the -hx option, which sounds 
like it might do exactly what your original post requested.

Additionally, -hbn and -hbm are quite useful for mapping out hydrogen bonds, and 
can be advantageously combined with index files for a more narrow view of things.

-Justin

> Anyway for the time being I am using this strategy. But if anyway has 
> other options then kindly let me know.
> 
> Thanks in advance,
> with warm regards,
> anil
> IIT Bombay
> India
> 
> On Sun, Sep 13, 2009 at 9:41 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     Anil Kumar wrote:
> 
>         Dear Gmx Users,
> 
>         I need to calculate the H-Bonds of simulation trajectory with
>         specification
>         of i to i+2/3/4/5 so on..and i to i -2/3/4/5 so on...separately.
> 
>         Do anyone have any idea how to do this...since the present
>         option g_hbond
>         calculate both the hydrogen bonds together irrespective of i to i+/-
>         2/3/4/5/6 and so on..
> 
>         Or is there any other program which can be used for this analysis.
> 
> 
>     Read g_hbond -h and/or consider creating suitable index groups with
>     make_ndx in an index file to pass to g_hbond using -n.
> 
>     Mark
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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