[gmx-users] unusual bonds

[Sudip Das]

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