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

[dipak sanap]

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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