[gmx-users] -pbc nojump failure

[Tsjerk Wassenaar]

No! You can't do that, because fitting will cause the PBC and the
coordinates to mismatch. So 'nojump' after that will for sure screw up the
coordinates. Check the trjconv workflow on the Gromacs site.

Cheers,

Tsjerk
On Mar 31, 2016 14:23, "Francesco Carbone" <fra.carbone8 at gmail.com> wrote:

> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump)
> later.
>
> Cheers,
>
> Fra
>
> On 31 March 2016 at 05:45, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> > Hi Irem,
> >
> > Check the structure in nvt_water_frozen.tpr:
> >
> > gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
> >
> > Cheers,
> >
> > Tsjerk
> > On Mar 31, 2016 00:04, "Irem Altan" <irem.altan at duke.edu> wrote:
> >
> > > Hi,
> > >
> > > I am simulating a protein in its unit cell. I use the original .pdb
> file
> > > as an input, so the initial molecule is not fragmented. At the end of
> the
> > > simulation, I generate a .pdb file containing the trajectory of the
> > protein
> > > as follows:
> > >
> > > gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc
> > > nojump -o prot.pdb
> > >
> > > Despite the fact that I use -pbc nojump, I still get all the
> coordinates
> > > wrapped into the unit cell, and therefore the protein fragmented. What
> > > could be wrong? (I use GROMACS 5.1.2)
> > >
> > > Best,
> > > Irem
> > > --
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