[gmx-users] trjconv -fit progressive

Justin Lemkul jalemkul at vt.edu
Fri Sep 8 17:59:43 CEST 2017

On 9/8/17 11:57 AM, edesantis wrote:
> Hi gromacs users,
> I removed the boundary effects on my system box during the trajectory 
> of protein crystal simulation following the Suggested trjconv workflow
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions 
> then I need to fit the trj to remove rotations and translations (my 
> propose is to reproduce a scattering pattern of the crystal, so I want 
> that all frames are superimposable)
> so I tough to use -fit rot+trans
> looking at the trjconv manual I've seen also the flag -fit progressive,
> but actually I didn't understand what does this operation do,
> do you know it?

It's described in the help info:

"There are two options for fitting the trajectory to a reference either for
essential dynamics analysis, etc. The first option is just plain fitting 
to a
reference structure in the structure file. The second option is a 
fit in which the first timeframe is fitted to the reference structure in the
structure file to obtain and each subsequent timeframe is fitted to the
previously fitted structure. This way a continuous trajectory is generated,
which might not be the case when using the regular fit method, e.g. when 
protein undergoes large conformational transitions."



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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