Hello developers,
I am simulation a long IDP with 58 residues. But when use the command
gmx trjconv -f production.xtc -n index.ndx -o trajout.xtc -pbc whole -center -s production.tpr
It gives me following error:
Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 790 atoms. The longest distance involved in such interactions is
9.511 nm which is above half the box length. This molecule type consists of
muliple 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.
I choose the box size of 3 nm.
Please guide me why this issue occure. Thanks in Advance.
I would think that the error is from the -center option. Try without it and see if it works. If it does, you might want to select only a few atoms, for centering, close to where you want to center instead of selecting the whole molecule.
By the way, according to the selections, there are 739 atoms in the protein. The error says that there are 790 atoms in the molecule type. Are the ions somehow included in the same molecule type as the protein? Could you post your topology (.top) file? You might have to rename it to, e.g., .txt.
It is not looking well. Due to PBC it has been broken. I am not understand the error. What it is calculated the “The longest distance involved in such interactions is 9.511 nm which is above half the box length.”
