[gmx-users] water stretched apart

[Chandan Choudhury]

Dear Chetan,
trjconv is finding difficult to find the trp file. Check that the tpr
yourare providing is in the right place.

Chandan
On Sun, May 11, 2014 at 1:33 PM, Chetan Mahajan <chetanvm10 at gmail.com>wrote:

> 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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-- 

--
Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India