[gmx-users] water stretched apart
chetanvm10 at gmail.com
Sun May 11 10:03:47 CEST 2014
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
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?
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.
> 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:
> > 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
> > 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
> > above. Can anyone throw light on what does it mean or why it is
> > 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
> > --
> > Gromacs Users mailing list
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users