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

Mon Nov 10 17:36:01 CET 2014

Hi Carlos,

You used -pbc nojump on the last frame with the .tpr as reference, which
means it removes the jumps with respect to the tpr, and that will give
rubbish. You should use -pbc mol and try again.

Cheers,

Tsjerk

On Mon, Nov 10, 2014 at 5:25 PM, Carlos Navarro Retamal <cnavarro at utalca.cl>
wrote:

> Dear Erick,
> First of all thanks a lot for your reply.
> Your are correct. I know that there’s not a ‘middle’ part in the system
> (based on the PBC), i was just trying to say that i need a structure where
> the protein will be surrounded by the POPC membrane in order to have
> ‘valid’ structure to start the AA MD simulations.
>
> I run the following commands:
>
> > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc nojump
> -o LastFrame.gro
> >
>
>
> followed by:
>
> > trjconv -f LastFrame.gro -s dynamic-NO-Elastic.tpr -fit rot+trans -o
> conf.gro
> >
>
> without luck ( the proteins is not fix either with these commands).
> what should i do?
>
>
> Dear Tsjerk,
> Thanks for your kind reply.
> I did what you suggested, without luck:
> > ./initram.sh -f LastFrame.gro -o aa_gromos54a7.gro -to gromos54a7 -p
> topol.top
> (in the input file the protein is intact)
> CG-model:
> http://cl.ly/3V3E1O2R0L31
> AA-model
> http://cl.ly/0U2r2n0F290i
>
>
> Thanks to both of you for all your help,
> 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 12:16 PM, Erik Marklund wrote:
>
> > 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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-- 
Tsjerk A. Wassenaar, Ph.D.