[gmx-users] water stretched apart

[Chetan Mahajan]

Dear Chandan,

Yes, .tpr file is in the same folder. I am not sure what's happening.

Thanks
Chetan


On Sun, May 11, 2014 at 3:17 AM, Chandan Choudhury <iitdckc at gmail.com>wrote:

> 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
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