[gmx-users] Coordinates transformation

Justin Lemkul jalemkul at vt.edu
Wed Aug 15 13:30:42 CEST 2018

On 8/15/18 5:47 AM, Yasser Almeida Hernández wrote:
> Hi all,
> I have two different simulations of a membrane protein in a E. coli 
> model membrane, and I want to analyze the protein-lipids interactions, 
> by generating 2D density maps. In each simulation, the protein 
> moves/rotates different along the xy plane of the membrane, and ends 
> up in a different orientation.
> Is there a way to transform the coordinates of one simulation, ex. 
> superposing one onto the other (taking the protein coordinates of the 
> first simulation as reference) to have both in the same coordinates 
> system and the proteins in the same orientation, so I can generate 
> comparable 2D maps?

Use trjconv -fit rotxy+transxy



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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