[gmx-users] Dynamics of the salt-bridges

[Justin Lemkul]

On 2/3/13 12:36 PM, James Starlight wrote:
> Justin,
>
> 1 )for example I want to select in index file only all asp, glu and
> his residues ( I could find selection by residue type only).
>

What you would do is create a complement to that group - keep all the Asp, Glu, 
and His charged and use -zeroq to remove charges on all other atoms.

> 2) Than I'd like that gromacs compute dynamics of the distance between
> that charge groups (providing only truncated .tpr file as the input)

Don't use a truncated .tpr file - you'll have problems.

> but only. Could other than g_saltbr gromacs tools be used for that
> (E,g g_dist ) ?
>

Yes, iterative calls to g_dist can easily be scripted.  In that case, though, 
we're talking about something different - you would need each residue (or 
representative atoms thereof) in its own separate group to measure distances 
between them.

-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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