[gmx-users] pbc problem

tarak karmakar tarak20489 at gmail.com
Wed Jan 29 11:27:40 CET 2014

trjconv -s topol.tpr -f traj -pbc mol -o traj_modified

select '0' for the entire system

You can try using either 'mol' or 'nojump' depending on your visualization


On Wed, Jan 29, 2014 at 3:39 PM, Atila Petrosian
<atila.petrosian at gmail.com>wrote:

> Dear Gromacs users
> I did simulation of a system containing protein and cnt using gromacs
> 4.5.6.
> When I see trajectory by VMD, in some frames, protein atoms exit one side
> of box
> and enter opposite side of box (pbc problem). I know I should use -pbc
> option of
> trjconv tool. But I do not know exactly which of none, mol, res, atom,
> nojump,
> cluster or whole is appropriate for me. The below link shows one frame of
> trajectory:
> https://www.dropbox.com/s/vur8fh1apvp79lm/pbc%20problem.bmp
> Any help will highly appreciated
> --
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