[gmx-users] water stretched apart

[Chetan Mahajan]

Thanks, Tsjerk. I tried it with following:

trjconv -pbc whole -f lnanop.xtc -s lnanop.tpr -o lnanoppbc.xtc

It gives the error : Cannot read from input

and

WARNING: If there are molecules in the input trajectory file
         that are broken across periodic boundaries, they
         cannot be made whole (or treated as whole) without
         you providing a run input file.

I read trjconv part of manual again and again, but can't figure out what's
going wrong. Could you help please?

Thanks
Chetan


On Sun, May 11, 2014 at 1:30 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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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