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Dear Experts,
I am trying to calculate protein backbone rmsd. But I got thr following error message.
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 50896 atoms. The longest distance involved in such interactions
is 6.694 nm which is above half the box length. This molecule type consists of
multiple parts, e.g. monomers, that are connected by interactions that are not
chemical bonds, e.g. restraints. Such systems can not be treated. The only
solution is increasing the box size.
Maybe you should use these commands to make sure there are no shifts over the periodic boundary conditions: First - gmx trjconv -s your_tpr.tpr -f your_traj.xtc -o whole.xtc -pbc mol
and then next - gmx trjconv -s your_tpr.tpr -f whole.xtc -o centered.xtc -center -pbc mol
Thank you for your response.
But when I type the command
gmx trjconv -s …/prod1.tpr -f …/40.xtc -o whole.xtc -pbc mol
I got the same error message.
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 50896 atoms. The longest distance involved in such interactions
is 6.694 nm which is above half the box length. This molecule type consists of
multiple parts, e.g. monomers, that are connected by interactions that are not
chemical bonds, e.g. restraints. Such systems can not be treated. The only
solution is increasing the box size
Thank you for your reply.
Yes, it is a cubic salvation box (8.0 nm).
I have already perform 40 ns production run.
Then I have to increase box size.
I type the following command.