I have face this problem anyone help me how to solve this issue ?which is below
Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 78 atoms. The longest distance involved in such interactions is
4.894 nm which is above half the box length. Either you have excessively large
distances between atoms in bonded interactions or your system is exploding.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
It seems like your box size might be too small compared to your short-range interaction cutoff, leading to issues with periodic boundary conditions.
Here are some key points to consider:
1. For short-range non-bonded interactions, only the nearest image of each particle is considered among all those generated by PBC.
2. A spherical cutoff is applied to limit the number of interactions calculated.
3. The cutoff radius shouldn’t be more than half the shortest box vector, or multiple images of a particle might fall within the cutoff distance.
4. Ideally, a solvent molecule shouldn’t interact with both sides of your macromolecule. Therefore, each box vector should be longer than the macromolecule by at least twice the cutoff radius.
To fix this error, you can adjust your box size using the GROMACS command to ensure there’s at least 1 nm between your protein and the box edge. Also, set your short-range cutoff to 9 or 10 Å in the MDP file.
- Badges
- Science topic
- Similar topics
- Filing