[gmx-users] Simulating a protein dimer

[Biplab Ghosh]

Dear Gromacs Users,

I am trying to simulate a protein dimer using Gromacs-5.1.2. Gromacs
completed successfully
but when analysing the trajectories, the monomers are flying apart and
coming back again!

I used the following Gromacs commands/options:

gmx trjconv -s protein-md.tpr -f protein-md.xtc  -pbc mol -center -ur
compact -o protein-md-center.xtc

gmx trjconv -s protein-md.tpr -f  protein-md-center.xtc -fit rot+trans -o
protein-md-center-fit.xtc

gmx trjconv -s protein-processed.gro -f protein-md-center-fit.xtc -o
protein-movie.pdb -tu ns -dt 1


I would really appreciate any help on this.

Regards,
Biplab.

--
"Simplicity in life allows you to focus on what's important"