[gmx-users] unusual bonds

[Mark Abraham]

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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