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

Tue Aug 23 16:43:38 CEST 2016

If you want to remove the pbc, you must use -pbc nojump.
-pbc mol will put everything in the pbc while having whole molecules
(molecules not cut by the pbc), that's all. I probably don't get what you
call "PBC removed" though.

For the analysis, it depends on your system (and what you want to analyze),
but yeah if the visualization of your trajectory is fine it should be fine.
I know I had problems centering on an oligomeric protein in the past, and I
had to use -pbc nojump before centering, and then putting everything back
in the box with -pbc mol (in 3 rounds of trjconv).

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 15:58 GMT+02:00 dipak sanap <dipak94sanap at gmail.com>:

> Hi, thanks for reply.
> If I understand correctly, one should not carry out multiple passes to
> achieve multiple conversions of trajectory. Here, I want both protein to be
> centered and PBC removed.
>
> So, instead of case 3, I did following and it keeps protein in the center.
>
> trjconv -s *.tpr -f *.xtc -center -o centered.xtc
> trjconv -s *.tpr -f centered.xtc -pbc mol -ur compact -o centered_noPBC.xtc
>
> Is resulting trajectory correct for analysis? Is there way to know if
> anything is wrong with trajectory if there is no problem in vmd
> visualization?
>
>
> On Tue, Aug 23, 2016 at 4:49 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > As
> > http://www.gromacs.org/Documentation/Terminology/
> > Periodic_Boundary_Conditions
> > suggests,
> > you may well need multiple passes of trjconv. The implementation
> hard-codes
> > the order of operations when you try to run more than one in the same
> call
> > to trjconv. If you want the "other" order, then you currently don't have
> an
> > option other than writing to disk and running trjconv again. I'd like to
> > make this easier to do, but that's a survey thread for another day :-)
> >
> > Mark
> >
> > On Tue, Aug 23, 2016 at 1:10 PM dipak sanap <dipak94sanap at gmail.com>
> > wrote:
> >
> > > Hello, thank you all for helping. As mentioned in my question, 3rd case
> > > gives desired result that is centering protein with dodecahedron
> > > visualization. So my question is, why first two step fail that first
> > > centering and then removal of PBC and vice versa, both dont give right
> > > answer but combination of centering and pdb works.
> > >
> > > On Tue, Aug 23, 2016 at 1:54 PM, Marlon Sidore <
> marlon.sidore at gmail.com>
> > > wrote:
> > >
> > > > 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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