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

Erik Marklund erik.marklund at chem.ox.ac.uk
Mon Nov 10 16:16:58 CET 2014


Dear Carlos,

I guess it's just not obvious to most of us why this is a problem at all. If the protein diffuses (as proteins do) you can just translate/rotate it back to where it was. Strictly speaking , there is no 'middle' in a periodic system. Or are we missing something?

In any case, adding restraints can affect the dynamics and you can often use trjconv -nojump followed by trjconv -fit to get your protein sit steadily in the middle of your box, assuming the protein was where you wanted it to be in the first place.

Kind regards,
Erik


Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 10 Nov 2014, at 15:01, Carlos Navarro Retamal <cnavarro at utalca.cl<mailto: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<mailto:carlos.navarro87 at gmail.com> or cnavarro at utalca.cl<mailto: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> (mailto:carlos.navarro87 at gmail.com) or cnavarro at utalca.cl<mailto:cnavarro at utalca.cl> (mailto:cnavarro at utalca.cl)

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