[gmx-users] Selections in gromacs

[Tuanan Lourenço]

Hi everyone,

I am trying to use the "gmx trjconv" to write a new trajectory from my
"main trajecetory" that contains just two molecules then they are close to
each other in a specific distance. The idea is to have a new trajectory
that contains these molecules in this specific distance in each frame and
use this to calculate different properties such as msd. I also tried to use
the "gmx select" with the option -ofpdb but this writes just an average of
the positions, not for each frame. Has someone has some idea about how I
can proceed?

Thank you
-- 
__________________________________________________
MSc. Tuanan C Lourenço
Ph.D Student Physical Chemistry - Universidade Federal Fluminense
Molecular Modelling and Computer Simullation Group - UFF
MOLMOD-CS WEBSITE <http://www.molmodcs.uff.br/>