[gmx-users] Problem - How to center a protein in a CG simulation

Carlos Navarro Retamal cnavarro at utalca.cl
Mon Nov 10 06:11:39 CET 2014

Dear gromacs users,  
I’m trying to replicate the following paper: http://www.nature.com/ncomms/2014/140708/ncomms5377/full/ncomms5377.html

On that way i:
- Create a CG (two different ones, with and without elastic-network restraints) representation of my K2P protein by using martinize.py
- I embedded it in a POPC bilayer membrane using insane.py
After some energy minimization and equilibration i run a 500ns MD of production.
The problem was that during both simulation the protein starts to move across the box to a different box.  
By using tryconv as follows:
> trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc mol -o LastFrame.gro

i was able to ‘fix’ the protein (fix the pbc issue of the protein), but its remains out of the box.
I even used -center keyword without luck.
And since i need a structure where the protein remains in the middle of the POPC membrane in order to perform the ‘backward’ step to obtain an AA representation of my system and perform a new MD simulation  i’m kind of stuck.
I don’t know what to do :/
Hope someone can help me.
Have a nice week,

Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl

More information about the gromacs.org_gmx-users mailing list