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

[Carlos Navarro Retamal]

nobody?  
if there is not a way to do this at this moment (after the simulation) is there a way to apply a restraint to maintain fix the protein in the middle of the POPC bilayer (other than elastic network) during the MD simulation in order to avoid this problem?
Best regards,
Carlos

--  
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


On Monday, November 10, 2014 at 2:11 AM, Carlos Navarro Retamal wrote:

> 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
>  
>  
> --  
> 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 (mailto:carlos.navarro87 at gmail.com) or cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)
>  
> --  
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