[gmx-users] trjconv and ions

[Joe Joe]

Thanks, that makes sense.

On Thu, Mar 25, 2010 at 12:15 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:

> Hi Joe,
>
> Probably you have a mismatch between your reference structure and the
> trajectory. So trjconv assumes coordinates associated with ions, while they
> actually belong to water.
>
> Hope it helps,
>
> Tsjerk
>
> On Mar 25, 2010 7:22 PM, "Joe Joe" <ilchorny at gmail.com> wrote:
>
> I am seeing weird behavior when I trjconv my trajectory containing NaCl,
> tip3p, and protein. I use the OPLSAA force field and octahedral PBCs.
>
> When I run
>
> trjconv -f traj.trr -s topol.tpr -pbc nojump -o trajout.xtc
>
> The ions in the output form clusters of three similarly charged ions in the
> shaped like a triangle. If I look at the non trjconved trajectory everything
> looks fine. Any thoughts?
>
>
>
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