Hello,
I am performing MD calculations on a COF with aqueous solutes. The input structure consists of the COF framework with one adsorbate and packed with water molecules at standard density. If I decrease the density of water and spread out the molecules, the simulation runs without problems. However, when I try to pack the water molecules close enough to simulate the standard density of water, the calculation terminates with errors during equilibration, saying:
“ERROR on proc 27: Bond atoms 742 745 missing on proc 27 at step 10 (src/ntopo_bond_all.cpp:61)”
I used the lammps-interface code to generate input and data files in all calculations. All of the water molecules and the adsorbate are correctly bound and there are no bonds between water, the adsorbate, or the COF. All water molecules are placed such that there are no bonds across the periodic boundary conditions. Although the placement of water molecules determines whether these errors arise, the errors in bonds occur for some of the atoms of the framework as well as atoms in water.
I am using LJ potentials with cutoff 12.5 Ang and a UFF force field. I have tested this simulation on multiple versions of Lammps, the newest being the Aug 2023 update.
Does the proximity of atoms outside a molecule effect bonds between atoms of that molecule? Thank you for any guidance you can provide.