[gmx-users] plot rmsd of single atom / residue

[Erik Lindahl]

Hi,

Create an index file with (at least) two groups. One group will be  
used for fitting the structures (e.g. Calpha atoms), and the other  
for analysis (e.g. your single atom or residue).

Provide this index file to g_rms, select the first group when asked  
for the fitting group, and the second as the group to calculate cRMS/ 
RMSD for.


The fitting is an integral part when calculating RMSD. If you fit a  
single atom the RMSD will always be 0.0, and if you fit a residue the  
RMSD will only cover internal fluctuations in that residue. Only you  
can determine what you really want to fit to.


You might want to take a look at the program g_rmsf too, which  
calculates the average amount of fluctuations for atoms, either  
around the starting state (default), or around an average structure  
you can determine e.g. with g_traj.

Cheers,

Erik


On Oct 17, 2006, at 6:01 PM, Viswanadham Sridhara wrote:

> May be you can build an index file which has that specific residue  
> or atom and use it.
> If not, definitely you can make trajectory with that single atom/  
> residue and then use g_rmsd to get what you want.
>
> I hope its clear.
>
> On 10/17/06, Guenter Fritz <guenter.fritz at uni-konstanz.de> wrote:
> Dear Viswanadham,
>
> I used g_rmsd but did not find out how to select a single atom or
> residue. I just got as far as the pre-defined groups in g_rmsd (groups
> 1-14).
> Is there something like a a "sub-option" ?
>
> > You mean you dint find g_rmsd subroutine or you dint know the way to
> > use g_rmsd?
> >
> > On 10/17/06, *Guenter Fritz* < guenter.fritz at uni-konstanz.de
> > <mailto:guenter.fritz at uni-konstanz.de>> wrote:
> >
> >     Dear all,
> >
> >     I want to extrat  a rmsd of a single atom or specific residue  
> from
> >     the
> >     md trajectory. Should be simple but I didn't dind it.
> >     Thanks,
> >     Guenter
> >
> >
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> >
> >
> >
> > --
> > Viswanadham Sridhara,
> > Research Assistant,
> > Old Dominion University,
> > Norfolk, Va-23529.
> >
> >--------------------------------------------------------------------- 
> ---
> >
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>
> --
> ***********************************
>
> Dr. Guenter Fritz
> Fachbereich Biologie
> Sektion Naturwissenschaften
> Universitaet Konstanz
>
> Universitaetsstrasse 10
> Postfach M665
> D-78457 Konstanz
>
> e-mail: Guenter.Fritz at uni-konstanz.de
>
> http:\\www.biologie.uni-konstanz.de\fritz
>
> Tel.: +49-(0)7531 88 3687
> Fax:  +49-(0)7531 88 2966
>
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>
>
> -- 
> Viswanadham Sridhara,
> Research Assistant,
> Old Dominion University,
> Norfolk, Va-23529.
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