[gmx-users] Dynamics of the salt-bridges

Justin Lemkul jalemkul at vt.edu
Sun Feb 3 18:59:35 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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