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

[Tsjerk Wassenaar]

Hi Carlos,

Who says it needs to be in the center for backward? It needs to be in one
piece, but doesn't need to be in te center. Backward understands PBC. It's
not stupid ;)

Cheers,

Tsjerk


On Mon, Nov 10, 2014 at 4:01 PM, Carlos Navarro Retamal <cnavarro at utalca.cl>
wrote:

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.