[gmx-users] trjconv -fit progressive

[edesantis]

thanks Justin for your quick responce

have a nice weekend
Emiliano


On 2017-09-08 17:59, Justin Lemkul wrote:
> 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 
> progressive
> 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 your
> protein undergoes large conformational transitions."
> 
> -Justin
> 
> --
> ==================================================
> 
> 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
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> 
> ==================================================

-- 
Emiliano De Santis