[gmx-users] g_rms and g_cluster

[Mark Abraham]

On 09/03/11, shahid nayeem  <msnayeem at gmail.com> wrote:
> Hi Justin
> If I make an index group with backbone and CA C N O group of the
> concerned residues and then do least square fitting then do this
> fitting is equivalent to backbone fitting first and then translating
> to coincide CA of the residue of interest. Is there any other
> programme developed for gromacs trajectory analysis where I can do
> backbone fitting first and then translate to coincide CA of residue of
> interest before calculating RMSD.
> 

Group-wise fitting subject to the constraint of particular atoms overlaid requires a quite different algorithm from plain group-wise fitting, and is not implemented. You can do the plain fit, calculate the relative displacement of one CA from another by hand, and do the corresponding translation with editconf, but I doubt you're going to learn anything...

Mark


> 
> Shahid Nayeem
> 
> On Thu, Feb 24, 2011 at 7:14 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> > shahid nayeem wrote:
> >>
> >> Dear All
> >>
> >> I want to calculate RMSD of one side chain residue from simulation
> >> trajectory after full backbone alignment as well as translating to
> >> coincide CA of the residue of interest. Is it possible to do with
> >> g_rms both backbone alignment as well as translating to coincide CA.
> >
> > Least-squares fitting is performed on whatever group you choose (i.e.
> > backbone), and the calculation group can then be whatever you want.  You can
> > use trjconv to do translational fitting, but I don't know that you can force
> > g_rms to always align this certain atom and still perform a backbone fit;
> > these two may work against one another, even if the difference is small.
> >
> >> Another clarification is that in gromacs g_cluster how can I use
> >> greedy algorithm for clustering.
> >
> > What is a "greedy" algorithm?  The available methods are described in the
> > manual and/or g_cluster -h.
> >
> > -Justin
> >
> >> Shahid Nayeem
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > 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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