[gmx-users] Dynamics of the salt-bridges

[Justin Lemkul]

On 2/1/13 3:22 PM, James Starlight wrote:
> Dear Gromacs users!
>
>
> I have trajectory from which I want to investigate dynamics of all
> possible salt bridges (E.g distance between adjacent + and - charged
> residues) of my protein during the simulation
>
> As I understood ussage of g_saltbr -t -sep could be suitable for such
> thing but I'm not sure in validness of -t for definition of the native
> salt bridges ( e.g with the default settings g_saltbr produced huge
> number of all possible combinations of the polar contacts within my
> protein ). Is there any others gromacs tols for such investigation?
>

Not really.  If you're looking for any possible combinations of charged 
residues, g_saltbr is the only way to go.  The default value of -t basically 
means everything is always considered, which you may not want.  A more 
physically relevant truncation distance is probably warranted, but it's been a 
long time since I've played with it.  You can always make subset trajectories 
(with matching .tpr files from tpbconv) to analyze smaller chunks of residues 
and ignore things you may not care about, like ions.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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