[gmx-users] -pbc nojump failure

[Francesco Carbone]

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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