Hi,
Im trying to run a CG MD on a small protein-rna complex to validate my actual run. For this im using the pdb 1MMS where i coarse grain protein and rna separately and just merge by cat. I have done all the steps up to solvating and adding ions, which have worked fine, but when I move on to the energy minimization i keep getting this error:
Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 143 atoms. The longest distance involved in such interactions is
6.191 nm which is above half the box length. Either you have excessively large
distances between atoms in bonded interactions or your system is exploding
Does anyone know how to fix this?