Inconsistent shifts

User discussions
1

GROMACS version: 2019.4
GROMACS modification: Yes with plumed

I have performed an MD run. The simulation has run smoothly without errors or warnings about inconsistent shifts (though it is not finished yet, as it stopped due to maxh option).

When I try to generate a trajectory with:

gmx_mpi trjconv -f prod_5/md.xtc -s prod_5/md.tpr -pbc whole -o prod5_prot.xtc

I get the following error:

Program:     gmx trjconv, version 2019.4
Source file: src/gromacs/pbcutil/mshift.cpp (line 917)

Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 543 atoms. The longest distance involved in such interactions is 4.286 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.

Does that mean there was a problem with the trajectory? Is there a way to solve it or I should start a new simulation from scratch. If so, what can be the cause of this error? I have run many similar simulations with other peptides without encountering this error.

Thanks for your time.

Ramon

2

Hi Ramon,

This error message indicates that some atoms will have to be moved more than half a box length to make the molecule whole, which might mean that whatever you simulated stretched out very long or wide in your simulation. To get something to visualise and understand what is happening you could use

gmx trjconv -pbc atom -ur compact

Maybe this helps you to get closer to what is happening.

gmx mindist -pi

might be helpful as well to get a first impression on what is going wrong.

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