[gmx-users] -pbc nojump failure

[Tsjerk Wassenaar]

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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