[gmx-users] water stretched apart

[Tsjerk Wassenaar]

Hi Chetan,

That's due to PBC. Use trjconv -pbc whole to fix it.

Cheers,

Tsjerk
On May 11, 2014 8:12 AM, "Chetan Mahajan" <chetanvm10 at gmail.com> wrote:

> Dear All,
>
> I need help interpreting one image, that I am sharing via a link:
>
>
> https://www.dropbox.com/s/z1dly0jfhlftcmc/Screen%20Shot%202014-05-11%20at%2012.46.56%20AM.png
>
> It's a system of TiO2 crystal ( 2160 atoms, positions restrained with
> refcoord-scaling: com), 1 formate ion, 1 sodium ion and 3656 water
> molecules, totaling 13133 atoms overall. As you can see TiO2 slab is at the
> center of the box. What I am concerned about is the few water molecules
> stretched along a long distance (visible via lines) in the snapshot shared
> above. Can anyone throw light on what does it mean or why it is happening?
> Is it bad totally? Any solution, if it is totally bad?
>
> I am using a timestep of 1 fs for entire simulation.
>
> Thank you very much.
>
> regards
> Chetan
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