[gmx-users] Monitoring of Salt bridges during simulation Run

[James Starlight]

Bharat, Peter thanks for advises

I've checked g_saltbr but not found possible definition of the specified
regions ( this utility lacks -n index.ndx option). How I could ignore
contacts between solvent and protein ?

Also what is the real *-t value should I provide ? As I understood this is
only Rmin but could I define Rmax cutoff as well?

James
*
5 апреля 2012 г. 12:36 пользователь Peter C. Lai <pcl at uab.edu> написал:

> g_saltbr?
>
> If you have salt bridges you already know about and want to look at, you
> can always go with g_dist per pair manually.
>
> On 2012-04-05 12:23:02PM +0400, James Starlight wrote:
> > Dear Gromacs Users!
> >
> >
> > I'd like to monitor origin and destabilisation of salt-bridges during
> > simulation time. In particular I want to define some charged residues
> > within selection groups to monitor both of intra-protein as well as
> > protein-protein interactions. In past I've used only
> > g_hbond<http://manual.gromacs.org/online/g_hbond.html>utillity to
> > monitor Hbonds within selection. Is there any specified program
> > for such task but with salt-bridges only ?
> >
> >
> > Thanks for help,
> >
> > James
>
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> --
> ==================================================================
> Peter C. Lai                    | University of Alabama-Birmingham
> Programmer/Analyst              | KAUL 752A
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