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

[Mark Abraham]

On 05/04/12, James Starlight <jmsstarlight at gmail.com> wrote:

> 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 ?

 
Use trjconv -n and tpbconv -n to create a matching subset of your trajectory and -s input file, and use that as input to g_saltbr. 
 

> 
> 
> 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?

 
Looks like Rmax to me, from g_saltbr -h, but if you experiment, find out and report back it can go into the next version of the documentation (which is never perfect!).
 
Mark 
 

> 
> 
> 
> 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
> > Genetics, Div. of Research      | 705 South 20th Street
> > pcl at uab.edu                     | Birmingham AL 35294-4461
> > (205) 690-0808                  |
> > ==================================================================
> > 
> > 
> > 
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> 

 
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