[gmx-users] about salt bridge

[Justin A. Lemkul]

xiongxuqiong wrote:
> 
> To whom it may concern，
>  
>       when I used g_saltbr to compute some salt bridges in my system, I 
> couldn't understand the option "-t".  The tutorial tell me that it's 
> trunc distance and the default is 1000. Then I want to find the 
> definition of the salt bridge in Gromacs. However, I couldn't find it.  
> Could you like to tell me the relative definition in Gromacs? And what 
> is a proper value for the option t?
>  

 From g_saltbr -h:

"A minimum distance can be given, (eg. the cut-off), then groups that are never 
closer than that distance will not be plotted."

Basically, if a salt bridge occurs within the truncation distance specified by 
-t, it will be plotted.  Using the default (1000 nm!) will capture all possible 
salt bridges in the system.

-Justin

>  
> Look forward to your early reply,
>  
> Regards,
> mary
> 2009-04-23
> 
> 
> 
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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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