[gmx-users] Remove PDB and center the protein.

[Marlon Sidore]

Usually, what works most of the time (haven't failed yet with this) is
first removing the PBC:

gmx trjconv -s inp.tpr -f inp.xtc -o nopbc.xtc -pbc nojump

And then centering:

gmx trjconv -s inp.tpr -f nopbc.xtc -o nopbc_center.xtc -center

If you later want the PBC back with the centered system, put everything
back in the box:

gmx trjconv -s inp.tpr -f nopbc_center.xtc -o center.xtc -pbc mol

If you also later want to fit the rotations of your centered thing, you'll
want to do it after this too.

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-08-23 9:38 GMT+02:00 Florent Hédin <work at fhedin.com>:

> Hi,
>
> I did something similar last month for a protein tetramer solvated using
> a truncated dodecahedron ;) Hope the following will help
>
> gmx trjconv -s inp.tpr -f inp.xtc -o clust.xtc -center -pbc clust
>
> gmx trjconv -s inp.tpr -f clust.xtc -o ok.xtc -center -pbc mol -ur compact
>
> As simulating a tetramer the key in my case was to use clust in the
> first step for pbc, otherwise I was also not able of properly centring
> the whole protein system.
>
> I don't know if it is useful to use center twice by hte way ; may be
> gromacs experts will know more.
>
> Cheers,
>
> Florent
>
> On 23/08/16 08:42, dipak sanap wrote:
> > HI all,
> >
> > I have simulated protein in a dodecahedron box. I know trjconv can be
> used
> > to center the protein and remove PBC but I am confused.
> >
> > I have tried few cases as follows.
> >
> > Case 1
> > trjconv -f *.xtc -s *.tpr -center -o centered.xtc
> > trjconv -f centered.xtc -s *.tpr -pbc mol -ur compact -o
> centered_noPBC.xtc
> >
> > Case 2
> > trjconv -f *.xtc -s *.tpr -pbc mol -ur compact -o noPBC.xtc
> > trjconv -f noPBC.xtc -s *.tpr -center -o centered_noPBC.xtc
> >
> > Case 3
> > trjconv -f *.xtc -s *.tpr -pbc mol -ur compact  -center -o
> > centered_noPBC.xtc
> >
> > In all cases, I use protein for centering and system for output. Only
> third
> > case keeps protein in center without jumping. What is the best way to
> > correct trajectory for both visualization and analysis?
> >
> > Regards,
> > Dipak
> >
>
> --
> Florent Hédin
> work at fhedin.com <mailto:work at fhedin.com>
> Public GPG KEY
> <https://pgp.mit.edu/pks/lookup?op=get&search=0xBAAE5B1AB2E702B4>
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