[gmx-users] jump problem

[Ahmet yıldırım]

Dear users,

I tried to remove the jumps of a structure after simulation but I couldn't
do it. The structure is heterodimer. I tried the following ways:

1)
-gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump
-gmx trjconv -f traj_nojump.xtc -s md.tpr -o traj_center.xtc -pbc mol -ur
compact -center

2)
 gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump -center

3)
-gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump -center
-gmx trjconv -f traj_nojump.xtc -s md.tpr -o traj_center.xtc -fit rot+trans

Do you have any suggestion(s)?

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Ahmet Yıldırım