[gmx-users] trjconv -fit progressive
edesantis at roma2.infn.it
Fri Sep 8 18:05:41 CEST 2017
thanks Justin for your quick responce
have a nice weekend
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
>> 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
>> 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
> 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
> which might not be the case when using the regular fit method, e.g.
> when your
> 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
Emiliano De Santis
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