[gmx-users] unusual bonds

[Sudip Das]

Hi Mark,

Thanks for your reply!

Sudip

On Mon, Feb 8, 2016 at 12:49 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> This is normal. Remember that vmd didn't read your topology file, it read a
> different .gro file each time and made different guesses about where bonds
> might be. See
> http://www.gromacs.org/Downloads/Related_Software/Visualization_Software
>
> Mark
>
> On Mon, Feb 8, 2016 at 6:58 AM Sudip Das <das.sudip37 at gmail.com> wrote:
>
> > Dear users,
> >
> > I am simulating a system composed of protein,ionic liquid and water in
> > gromacs 5.0.2 (double precision). I am facing a problem listed below.
> >
> > 1.  trjconv_mpi_d -f trj.xtc -s run.tpr -o trj_unwrap.xtc -pbc mol
> >
> >      vmd trj_unwrap.xtc frame_before_run.gro
> >
> >      This is showing two unusual bonds.
> >
> > 2.  vmd trj_unwrap.xtc frame_after_run.gro
> >
> >      This is showing 10 unusual bonds, but here the residues, which are
> > forming before two unusual        bonds, are not involved.
> >
> > 3. trjconv_mpi_d -f trj.xtc -s run.tpr -o trj_unwrap.gro -pbc mol
> >
> >      vmd trj_unwrap.gro
> >
> >      This is showing 10 unusual bonds, but here the residues, which are
> > forming before two unusual        bonds, are not involved.
> >
> > 4. trjconv_mpi_d -f trj.xtc -s run.tpr -o trj_unwrap.pdb -pbc mol
> >
> >      vmd trj_unwrap.pdb
> >
> >      This is showing a large number of unusual bonds.
> >
> >
> >
> > Can anyone please sort out this problem?
> >
> > Thanks in advance,
> > Sudip
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